[med-svn] [Git][med-team/python-questplus][upstream] New upstream version 2023.1
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jul 16 10:36:51 BST 2024
Andreas Tille pushed to branch upstream at Debian Med / python-questplus
Commits:
d015787f by Andreas Tille at 2024-07-16T10:37:37+02:00
New upstream version 2023.1
- - - - -
21 changed files:
- − .appveyor.yml
- + .github/workflows/main.yml
- + .github/workflows/release.yml
- .readthedocs.yml
- − .travis.yml
- + BUILDING.md
- CHANGES.md
- MANIFEST.in
- doc/source/conf.py
- doc/source/installation.md
- + pyproject.toml
- questplus/__init__.py
- − questplus/_version.py
- − questplus/demos/__init__.py
- questplus/psychometric_function.py
- questplus/qp.py
- questplus/tests/test_qp.py
- questplus/utils.py
- − setup.cfg
- − setup.py
- − versioneer.py
Changes:
=====================================
.appveyor.yml deleted
=====================================
@@ -1,37 +0,0 @@
-build: off
-
-environment:
- MINICONDA: C:\\Miniconda3-x64
- matrix:
- - CONDA_PYTHON_VERSION: "3.6"
- - CONDA_PYTHON_VERSION: "3.7"
- - CONDA_PYTHON_VERSION: "3.8"
-
-init:
- - "ECHO %CONDA_PYTHON_VERSION% %MINICONDA%"
- - call %MINICONDA%\Scripts\activate.bat
- - conda config --set always_yes yes --set changeps1 no
- - conda update -q conda
- - conda info -a
- - "conda create -n questplus -c conda-forge python=%CONDA_PYTHON_VERSION% pytest numpy scipy xarray json_tricks"
- - call conda activate questplus
-# - conda list
-
-install:
- - python setup.py build
-
- # Build & install sdist.
- - python setup.py sdist --formats=zip
-# - pip install --no-deps dist/questplus-*.zip
-# - pip uninstall --yes questplus
-
- # Build & install wheel.
- - python setup.py bdist_wheel
-# - pip install --no-deps dist/questplus-*.whl
-# - pip uninstall --yes questplus
-
- - ps: Remove-Item –path dist, build –recurse
- - pip install --no-deps .
-
-test_script:
- - py.test
=====================================
.github/workflows/main.yml
=====================================
@@ -0,0 +1,60 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit tests
+
+on:
+ # push:
+ # branches: ['**']
+ pull_request:
+ branches: ['**']
+ create:
+ branches: [main]
+ tags: ['**']
+ # schedule:
+ # - cron: "0 4 * * *"
+
+jobs:
+ test:
+
+ strategy:
+ fail-fast: false
+ matrix:
+ python-version: ["3.8", "3.9", "3.10", "3.11"]
+ os: [ubuntu-latest, windows-latest, macos-latest]
+
+ runs-on: ${{ matrix.os }}
+
+ defaults:
+ run:
+ shell: bash
+
+ steps:
+ - uses: actions/checkout at v3
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python at v4
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip wheel build
+ python -m pip install pytest
+ - name: Build sdist
+ run: python -m build --sdist
+ - name: Install sdist
+ run: |
+ pip install --no-deps dist/questplus-*.*
+ pip uninstall --yes questplus
+ rm -rf dist
+ - name: Build wheel
+ run: python -m build --wheel
+ - name: Install wheel
+ run: |
+ pip install --no-deps dist/questplus-*.*
+ pip uninstall --yes questplus
+ rm -rf dist
+ - name: Install questplus
+ run: pip install .
+ - name: Test with pytest
+ run: |
+ pytest
=====================================
.github/workflows/release.yml
=====================================
@@ -0,0 +1,56 @@
+# Upload a Python Package using Twine when a release is created
+
+name: Build
+on:
+ release:
+ types: [published]
+ push:
+ branches:
+ - main
+ pull_request:
+ branches:
+ - main
+
+permissions:
+ contents: read
+
+jobs:
+ package:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout at v3
+ - name: Set up Python
+ uses: actions/setup-python at v4
+ with:
+ python-version: '3.11'
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install build twine
+ - name: Build package
+ run: python -m build --sdist --wheel
+ - name: Check package
+ run: twine check --strict dist/*
+ - name: Check env vars
+ run: |
+ echo "Triggered by: ${{ github.event_name }}"
+ - uses: actions/upload-artifact at v3
+ with:
+ name: dist
+ path: dist
+
+ # PyPI on release
+ pypi:
+ needs: package
+ runs-on: ubuntu-latest
+ if: github.event_name == 'release'
+ steps:
+ - uses: actions/download-artifact at v3
+ with:
+ name: dist
+ path: dist
+ - name: Publish to PyPI
+ uses: pypa/gh-action-pypi-publish at release/v1
+ with:
+ user: __token__
+ password: ${{ secrets.PYPI_API_TOKEN }}
=====================================
.readthedocs.yml
=====================================
@@ -4,7 +4,7 @@ sphinx:
configuration: doc/source/conf.py
python:
- version: 3.7
+ version: 3.10
install:
- requirements: doc/requirements-rtd.txt
- method: pip
=====================================
.travis.yml deleted
=====================================
@@ -1,56 +0,0 @@
-matrix:
- include:
- - os: linux
- env: CONDA_PYTHON_VERSION=3.6
-
- - os: linux
- env: CONDA_PYTHON_VERSION=3.7
-
- - os: linux
- env: CONDA_PYTHON_VERSION=3.8
-
- - os: osx
- env: CONDA_PYTHON_VERSION=3.6
-
- - os: osx
- env: CONDA_PYTHON_VERSION=3.7
-
- - os: osx
- env: CONDA_PYTHON_VERSION=3.8
-
-before_install:
- - echo "Installing Miniconda environment..."
- - if [ $TRAVIS_OS_NAME == 'linux' ];
- then export MINICONDA_URL=https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh;
- else export MINICONDA_URL=https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh;
- fi
- - wget $MINICONDA_URL -O miniconda.sh
- - bash miniconda.sh -b -p $HOME/miniconda
- - source ~/miniconda/etc/profile.d/conda.sh # Initialize shell.
- - hash -r
- - conda config --set always_yes yes --set changeps1 no
- - conda update -q conda
- - conda info -a
- - conda create -n questplus -c conda-forge python=$CONDA_PYTHON_VERSION pytest numpy scipy xarray json_tricks
- - conda activate questplus
- - conda list
-
-install:
- - python setup.py build
-
- # Build & install sdist.
- - python setup.py sdist
- - pip install --no-deps dist/questplus-*.tar.gz
- - pip uninstall --yes questplus
-
- # Build & install wheel.
- - python setup.py bdist_wheel
- - pip install --no-deps dist/questplus-*.whl
- - pip uninstall --yes questplus
-
- - rm -rf dist/ build/
-
- - pip install --no-deps .
-
-script:
- - py.test
=====================================
BUILDING.md
=====================================
@@ -0,0 +1,8 @@
+## Building a release
+
+* Create `sdist` and `wheel` distributions:
+ ```python
+ python -m build --sdist --wheel
+ ```
+ (optionally append `--no-isolation` if running into group policy
+ permission errors on managed Windows systems)
=====================================
CHANGES.md
=====================================
@@ -1,13 +1,27 @@
+Changes
+=======
+
+v2023.1
+--------
+
+* Fix definition of `norm_cdf` psychometric function, by [Alex Forrence](https://github.com/aforren1)
+* Ensure compatibility with latest from NumPy and xarray versions
+* Add Thurstone scaling
+* Minimal required Python version is now 3.8
+
v2019.4
-------
+
* Allow JSON serialization of random number generator
v2019.3
-------
+
* Allow to pass a prior when instantiating `QuestPlusWeibull`
v2019.2
-------
+
* Allow passing a random seed via `stim_selection_options` keyword
argument
* Better handling of `stim_selection_options` defaults (now allows
@@ -15,6 +29,7 @@ v2019.2
v2019.1
-------
+
* Allow to pass priors for only some parameters
(the remaining parameters will be assigned an uninformative prior)
* Add more docstrings, fix typo in usage example
@@ -22,5 +37,6 @@ v2019.1
v0.0.5
------
+
* Allow retrieval of marginal posterior PDFs via `QuestPlus.marginal_posterior`
* Allow `nan` values in JSON output (violating JSON std but useful)
=====================================
MANIFEST.in
=====================================
@@ -1,5 +1,3 @@
include LICENSE
include AUTHORS
include README.md
-include versioneer.py
-include questplus/_version.py
=====================================
doc/source/conf.py
=====================================
@@ -7,28 +7,29 @@
import os
import sys
-abs_path = os.path.abspath('../../questplus')
+abs_path = os.path.abspath("../../questplus")
assert os.path.exists(abs_path)
sys.path.insert(0, abs_path)
# -- Project information -----------------------------------------------------
-project = 'questplus'
-copyright = '2019, Richard Höchenberger'
-author = 'Richard Höchenberger'
+project = "questplus"
+copyright = "2019, Richard Höchenberger"
+author = "Richard Höchenberger"
-extensions = ['recommonmark', # markdown support
- 'sphinx.ext.autodoc',
- 'sphinx.ext.autosummary',
- # 'sphinx.ext.viewcode',
- 'sphinx.ext.napoleon',
- 'sphinx_autodoc_typehints', # needs to be loaded AFTER napoleon
- # 'sphinx.ext.coverage'
- ]
+extensions = [
+ "recommonmark", # markdown support
+ "sphinx.ext.autodoc",
+ "sphinx.ext.autosummary",
+ # 'sphinx.ext.viewcode',
+ "sphinx.ext.napoleon",
+ "sphinx_autodoc_typehints", # needs to be loaded AFTER napoleon
+ # 'sphinx.ext.coverage'
+]
# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
@@ -41,11 +42,11 @@ exclude_patterns = []
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
-autoclass_content = 'both' # Document __init__() methods as well.
+autoclass_content = "both" # Document __init__() methods as well.
=====================================
doc/source/installation.md
=====================================
@@ -2,7 +2,7 @@
### Requirements
-- Python 3.6+
+- Python 3.8+
- `xarray`
- `scipy`
- `json_tricks`
=====================================
pyproject.toml
=====================================
@@ -0,0 +1,43 @@
+[project]
+name = "questplus"
+description = "A QUEST+ implementation in Python."
+readme = "README.md"
+requires-python = ">=3.8"
+license = {file = "LICENSE"}
+keywords = ["science", "neuroscience", "psychology", "staircase"]
+authors = [
+ {name = "Richard Höchenberger"},
+ {email = "richard.hoechenberger at gmail.com"}
+]
+classifiers = [
+ "Intended Audience :: Science/Research",
+ "Programming Language :: Python"
+]
+dependencies = [
+ "numpy",
+ "scipy",
+ "xarray",
+ "json_tricks"
+]
+dynamic = ["version"]
+
+[build-system]
+requires = ["setuptools>=45", "setuptools_scm[toml]>=6.2", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+
+[tool.black]
+target-version = ['py38']
+include = '\.pyi?$'
+# 'extend-exclude' excludes files or directories in addition to the defaults
+extend-exclude = '''
+(
+ | ^/questplus/tests/
+)
+'''
+
+[tool.pytest.ini_options]
+filterwarnings = [
+ "error"
+]
=====================================
questplus/__init__.py
=====================================
@@ -1,5 +1,9 @@
-from .qp import QuestPlus, QuestPlusWeibull
+from importlib.metadata import version, PackageNotFoundError
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
+try:
+ __version__ = version("questplus")
+except PackageNotFoundError:
+ # package is not installed
+ pass
+
+from .qp import QuestPlus, QuestPlusWeibull, QuestPlusThurstone # noqa: F401
=====================================
questplus/_version.py deleted
=====================================
@@ -1,520 +0,0 @@
-
-# This file helps to compute a version number in source trees obtained from
-# git-archive tarball (such as those provided by githubs download-from-tag
-# feature). Distribution tarballs (built by setup.py sdist) and build
-# directories (produced by setup.py build) will contain a much shorter file
-# that just contains the computed version number.
-
-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
-
-"""Git implementation of _version.py."""
-
-import errno
-import os
-import re
-import subprocess
-import sys
-
-
-def get_keywords():
- """Get the keywords needed to look up the version information."""
- # these strings will be replaced by git during git-archive.
- # setup.py/versioneer.py will grep for the variable names, so they must
- # each be defined on a line of their own. _version.py will just call
- # get_keywords().
- git_refnames = " (HEAD -> master, tag: 2019.4)"
- git_full = "9abd28b7a64e1a7ded530b9603361842ee873859"
- git_date = "2019-12-24 19:07:26 +0100"
- keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
- return keywords
-
-
-class VersioneerConfig:
- """Container for Versioneer configuration parameters."""
-
-
-def get_config():
- """Create, populate and return the VersioneerConfig() object."""
- # these strings are filled in when 'setup.py versioneer' creates
- # _version.py
- cfg = VersioneerConfig()
- cfg.VCS = "git"
- cfg.style = "pep440"
- cfg.tag_prefix = ""
- cfg.parentdir_prefix = "None"
- cfg.versionfile_source = "questplus/_version.py"
- cfg.verbose = False
- return cfg
-
-
-class NotThisMethod(Exception):
- """Exception raised if a method is not valid for the current scenario."""
-
-
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
-
-def register_vcs_handler(vcs, method): # decorator
- """Decorator to mark a method as the handler for a particular VCS."""
- def decorate(f):
- """Store f in HANDLERS[vcs][method]."""
- if vcs not in HANDLERS:
- HANDLERS[vcs] = {}
- HANDLERS[vcs][method] = f
- return f
- return decorate
-
-
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
- env=None):
- """Call the given command(s)."""
- assert isinstance(commands, list)
- p = None
- for c in commands:
- try:
- dispcmd = str([c] + args)
- # remember shell=False, so use git.cmd on windows, not just git
- p = subprocess.Popen([c] + args, cwd=cwd, env=env,
- stdout=subprocess.PIPE,
- stderr=(subprocess.PIPE if hide_stderr
- else None))
- break
- except EnvironmentError:
- e = sys.exc_info()[1]
- if e.errno == errno.ENOENT:
- continue
- if verbose:
- print("unable to run %s" % dispcmd)
- print(e)
- return None, None
- else:
- if verbose:
- print("unable to find command, tried %s" % (commands,))
- return None, None
- stdout = p.communicate()[0].strip()
- if sys.version_info[0] >= 3:
- stdout = stdout.decode()
- if p.returncode != 0:
- if verbose:
- print("unable to run %s (error)" % dispcmd)
- print("stdout was %s" % stdout)
- return None, p.returncode
- return stdout, p.returncode
-
-
-def versions_from_parentdir(parentdir_prefix, root, verbose):
- """Try to determine the version from the parent directory name.
-
- Source tarballs conventionally unpack into a directory that includes both
- the project name and a version string. We will also support searching up
- two directory levels for an appropriately named parent directory
- """
- rootdirs = []
-
- for i in range(3):
- dirname = os.path.basename(root)
- if dirname.startswith(parentdir_prefix):
- return {"version": dirname[len(parentdir_prefix):],
- "full-revisionid": None,
- "dirty": False, "error": None, "date": None}
- else:
- rootdirs.append(root)
- root = os.path.dirname(root) # up a level
-
- if verbose:
- print("Tried directories %s but none started with prefix %s" %
- (str(rootdirs), parentdir_prefix))
- raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
- at register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
- """Extract version information from the given file."""
- # the code embedded in _version.py can just fetch the value of these
- # keywords. When used from setup.py, we don't want to import _version.py,
- # so we do it with a regexp instead. This function is not used from
- # _version.py.
- keywords = {}
- try:
- f = open(versionfile_abs, "r")
- for line in f.readlines():
- if line.strip().startswith("git_refnames ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["refnames"] = mo.group(1)
- if line.strip().startswith("git_full ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["full"] = mo.group(1)
- if line.strip().startswith("git_date ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["date"] = mo.group(1)
- f.close()
- except EnvironmentError:
- pass
- return keywords
-
-
- at register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
- """Get version information from git keywords."""
- if not keywords:
- raise NotThisMethod("no keywords at all, weird")
- date = keywords.get("date")
- if date is not None:
- # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
- # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
- # -like" string, which we must then edit to make compliant), because
- # it's been around since git-1.5.3, and it's too difficult to
- # discover which version we're using, or to work around using an
- # older one.
- date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
- refnames = keywords["refnames"].strip()
- if refnames.startswith("$Format"):
- if verbose:
- print("keywords are unexpanded, not using")
- raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
- refs = set([r.strip() for r in refnames.strip("()").split(",")])
- # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
- # just "foo-1.0". If we see a "tag: " prefix, prefer those.
- TAG = "tag: "
- tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
- if not tags:
- # Either we're using git < 1.8.3, or there really are no tags. We use
- # a heuristic: assume all version tags have a digit. The old git %d
- # expansion behaves like git log --decorate=short and strips out the
- # refs/heads/ and refs/tags/ prefixes that would let us distinguish
- # between branches and tags. By ignoring refnames without digits, we
- # filter out many common branch names like "release" and
- # "stabilization", as well as "HEAD" and "master".
- tags = set([r for r in refs if re.search(r'\d', r)])
- if verbose:
- print("discarding '%s', no digits" % ",".join(refs - tags))
- if verbose:
- print("likely tags: %s" % ",".join(sorted(tags)))
- for ref in sorted(tags):
- # sorting will prefer e.g. "2.0" over "2.0rc1"
- if ref.startswith(tag_prefix):
- r = ref[len(tag_prefix):]
- if verbose:
- print("picking %s" % r)
- return {"version": r,
- "full-revisionid": keywords["full"].strip(),
- "dirty": False, "error": None,
- "date": date}
- # no suitable tags, so version is "0+unknown", but full hex is still there
- if verbose:
- print("no suitable tags, using unknown + full revision id")
- return {"version": "0+unknown",
- "full-revisionid": keywords["full"].strip(),
- "dirty": False, "error": "no suitable tags", "date": None}
-
-
- at register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
- """Get version from 'git describe' in the root of the source tree.
-
- This only gets called if the git-archive 'subst' keywords were *not*
- expanded, and _version.py hasn't already been rewritten with a short
- version string, meaning we're inside a checked out source tree.
- """
- GITS = ["git"]
- if sys.platform == "win32":
- GITS = ["git.cmd", "git.exe"]
-
- out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
- hide_stderr=True)
- if rc != 0:
- if verbose:
- print("Directory %s not under git control" % root)
- raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
- # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
- # if there isn't one, this yields HEX[-dirty] (no NUM)
- describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
- "--always", "--long",
- "--match", "%s*" % tag_prefix],
- cwd=root)
- # --long was added in git-1.5.5
- if describe_out is None:
- raise NotThisMethod("'git describe' failed")
- describe_out = describe_out.strip()
- full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
- if full_out is None:
- raise NotThisMethod("'git rev-parse' failed")
- full_out = full_out.strip()
-
- pieces = {}
- pieces["long"] = full_out
- pieces["short"] = full_out[:7] # maybe improved later
- pieces["error"] = None
-
- # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
- # TAG might have hyphens.
- git_describe = describe_out
-
- # look for -dirty suffix
- dirty = git_describe.endswith("-dirty")
- pieces["dirty"] = dirty
- if dirty:
- git_describe = git_describe[:git_describe.rindex("-dirty")]
-
- # now we have TAG-NUM-gHEX or HEX
-
- if "-" in git_describe:
- # TAG-NUM-gHEX
- mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
- if not mo:
- # unparseable. Maybe git-describe is misbehaving?
- pieces["error"] = ("unable to parse git-describe output: '%s'"
- % describe_out)
- return pieces
-
- # tag
- full_tag = mo.group(1)
- if not full_tag.startswith(tag_prefix):
- if verbose:
- fmt = "tag '%s' doesn't start with prefix '%s'"
- print(fmt % (full_tag, tag_prefix))
- pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
- % (full_tag, tag_prefix))
- return pieces
- pieces["closest-tag"] = full_tag[len(tag_prefix):]
-
- # distance: number of commits since tag
- pieces["distance"] = int(mo.group(2))
-
- # commit: short hex revision ID
- pieces["short"] = mo.group(3)
-
- else:
- # HEX: no tags
- pieces["closest-tag"] = None
- count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
- cwd=root)
- pieces["distance"] = int(count_out) # total number of commits
-
- # commit date: see ISO-8601 comment in git_versions_from_keywords()
- date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
- cwd=root)[0].strip()
- pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-
- return pieces
-
-
-def plus_or_dot(pieces):
- """Return a + if we don't already have one, else return a ."""
- if "+" in pieces.get("closest-tag", ""):
- return "."
- return "+"
-
-
-def render_pep440(pieces):
- """Build up version string, with post-release "local version identifier".
-
- Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
- get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
- Exceptions:
- 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += plus_or_dot(pieces)
- rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
- if pieces["dirty"]:
- rendered += ".dirty"
- else:
- # exception #1
- rendered = "0+untagged.%d.g%s" % (pieces["distance"],
- pieces["short"])
- if pieces["dirty"]:
- rendered += ".dirty"
- return rendered
-
-
-def render_pep440_pre(pieces):
- """TAG[.post.devDISTANCE] -- No -dirty.
-
- Exceptions:
- 1: no tags. 0.post.devDISTANCE
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"]:
- rendered += ".post.dev%d" % pieces["distance"]
- else:
- # exception #1
- rendered = "0.post.dev%d" % pieces["distance"]
- return rendered
-
-
-def render_pep440_post(pieces):
- """TAG[.postDISTANCE[.dev0]+gHEX] .
-
- The ".dev0" means dirty. Note that .dev0 sorts backwards
- (a dirty tree will appear "older" than the corresponding clean one),
- but you shouldn't be releasing software with -dirty anyways.
-
- Exceptions:
- 1: no tags. 0.postDISTANCE[.dev0]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += ".post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- rendered += plus_or_dot(pieces)
- rendered += "g%s" % pieces["short"]
- else:
- # exception #1
- rendered = "0.post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- rendered += "+g%s" % pieces["short"]
- return rendered
-
-
-def render_pep440_old(pieces):
- """TAG[.postDISTANCE[.dev0]] .
-
- The ".dev0" means dirty.
-
- Eexceptions:
- 1: no tags. 0.postDISTANCE[.dev0]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += ".post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- else:
- # exception #1
- rendered = "0.post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- return rendered
-
-
-def render_git_describe(pieces):
- """TAG[-DISTANCE-gHEX][-dirty].
-
- Like 'git describe --tags --dirty --always'.
-
- Exceptions:
- 1: no tags. HEX[-dirty] (note: no 'g' prefix)
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"]:
- rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
- else:
- # exception #1
- rendered = pieces["short"]
- if pieces["dirty"]:
- rendered += "-dirty"
- return rendered
-
-
-def render_git_describe_long(pieces):
- """TAG-DISTANCE-gHEX[-dirty].
-
- Like 'git describe --tags --dirty --always -long'.
- The distance/hash is unconditional.
-
- Exceptions:
- 1: no tags. HEX[-dirty] (note: no 'g' prefix)
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
- else:
- # exception #1
- rendered = pieces["short"]
- if pieces["dirty"]:
- rendered += "-dirty"
- return rendered
-
-
-def render(pieces, style):
- """Render the given version pieces into the requested style."""
- if pieces["error"]:
- return {"version": "unknown",
- "full-revisionid": pieces.get("long"),
- "dirty": None,
- "error": pieces["error"],
- "date": None}
-
- if not style or style == "default":
- style = "pep440" # the default
-
- if style == "pep440":
- rendered = render_pep440(pieces)
- elif style == "pep440-pre":
- rendered = render_pep440_pre(pieces)
- elif style == "pep440-post":
- rendered = render_pep440_post(pieces)
- elif style == "pep440-old":
- rendered = render_pep440_old(pieces)
- elif style == "git-describe":
- rendered = render_git_describe(pieces)
- elif style == "git-describe-long":
- rendered = render_git_describe_long(pieces)
- else:
- raise ValueError("unknown style '%s'" % style)
-
- return {"version": rendered, "full-revisionid": pieces["long"],
- "dirty": pieces["dirty"], "error": None,
- "date": pieces.get("date")}
-
-
-def get_versions():
- """Get version information or return default if unable to do so."""
- # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
- # __file__, we can work backwards from there to the root. Some
- # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
- # case we can only use expanded keywords.
-
- cfg = get_config()
- verbose = cfg.verbose
-
- try:
- return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
- verbose)
- except NotThisMethod:
- pass
-
- try:
- root = os.path.realpath(__file__)
- # versionfile_source is the relative path from the top of the source
- # tree (where the .git directory might live) to this file. Invert
- # this to find the root from __file__.
- for i in cfg.versionfile_source.split('/'):
- root = os.path.dirname(root)
- except NameError:
- return {"version": "0+unknown", "full-revisionid": None,
- "dirty": None,
- "error": "unable to find root of source tree",
- "date": None}
-
- try:
- pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
- return render(pieces, cfg.style)
- except NotThisMethod:
- pass
-
- try:
- if cfg.parentdir_prefix:
- return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
- except NotThisMethod:
- pass
-
- return {"version": "0+unknown", "full-revisionid": None,
- "dirty": None,
- "error": "unable to compute version", "date": None}
=====================================
questplus/demos/__init__.py deleted
=====================================
=====================================
questplus/psychometric_function.py
=====================================
@@ -1,17 +1,20 @@
from typing import Union, Iterable
import numpy as np
+from numpy.typing import ArrayLike
import scipy.stats
import xarray as xr
-def weibull(*,
- intensity: Union[float, Iterable[float]],
- threshold: Union[float, Iterable[float]],
- slope: Union[float, Iterable[float]] = 3.5,
- lower_asymptote: Union[float, Iterable[float]] = 0.01,
- lapse_rate: Union[float, Iterable[float]] = 0.01,
- scale: str = 'log10') -> xr.DataArray:
- """
+def weibull(
+ *,
+ intensity: Union[float, Iterable[float]],
+ threshold: Union[float, Iterable[float]],
+ slope: Union[float, Iterable[float]] = 3.5,
+ lower_asymptote: Union[float, Iterable[float]] = 0.01,
+ lapse_rate: Union[float, Iterable[float]] = 0.01,
+ scale: str = "log10",
+) -> xr.DataArray:
+ r"""
A Weibull psychometric function.
Parameters
@@ -75,46 +78,53 @@ def weibull(*,
# lapse_rate,
# indexing='ij', sparse=True)
- x = xr.DataArray(data=intensity, dims=['intensity'],
- coords=dict(intensity=intensity))
- t = xr.DataArray(data=threshold, dims=['threshold'],
- coords=dict(threshold=threshold))
- beta = xr.DataArray(data=slope, dims=['slope'],
- coords=dict(slope=slope))
- gamma = xr.DataArray(data=lower_asymptote, dims=['lower_asymptote'],
- coords=dict(lower_asymptote=lower_asymptote))
- delta = xr.DataArray(data=lapse_rate, dims=['lapse_rate'],
- coords=dict(lapse_rate=lapse_rate))
+ x = xr.DataArray(
+ data=intensity, dims=["intensity"], coords=dict(intensity=intensity)
+ )
+ t = xr.DataArray(
+ data=threshold, dims=["threshold"], coords=dict(threshold=threshold)
+ )
+ beta = xr.DataArray(data=slope, dims=["slope"], coords=dict(slope=slope))
+ gamma = xr.DataArray(
+ data=lower_asymptote,
+ dims=["lower_asymptote"],
+ coords=dict(lower_asymptote=lower_asymptote),
+ )
+ delta = xr.DataArray(
+ data=lapse_rate, dims=["lapse_rate"], coords=dict(lapse_rate=lapse_rate)
+ )
assert np.atleast_1d(x.squeeze()).shape == np.atleast_1d(intensity).shape
assert np.atleast_1d(t.squeeze()).shape == np.atleast_1d(threshold).shape
assert np.atleast_1d(beta.squeeze()).shape == np.atleast_1d(slope).shape
assert np.atleast_1d(gamma.squeeze()).shape == np.atleast_1d(lower_asymptote).shape
assert np.atleast_1d(delta.squeeze()).shape == np.atleast_1d(lapse_rate).shape
- if scale == 'linear':
- p = 1 - delta - (1 - gamma - delta) * np.exp(-(x / t)**beta)
- elif scale == 'log10':
- p = 1 - delta - (1 - gamma - delta) * np.exp(-10 ** (beta * (x - t)))
- elif scale == 'dB':
- p = 1 - delta - (1 - gamma - delta) * np.exp(-10 ** (beta * (x - t) / 20))
+ if scale == "linear":
+ p = 1 - delta - (1 - gamma - delta) * np.exp(-((x / t) ** beta))
+ elif scale == "log10":
+ p = 1 - delta - (1 - gamma - delta) * np.exp(-(10 ** (beta * (x - t))))
+ elif scale == "dB":
+ p = 1 - delta - (1 - gamma - delta) * np.exp(-(10 ** (beta * (x - t) / 20)))
else:
- raise ValueError('Invalid scale specified.')
+ raise ValueError("Invalid scale specified.")
return p
-def csf(*,
- contrast: Union[float, Iterable[float]],
- spatial_freq: Union[float, Iterable[float]],
- temporal_freq: Union[float, Iterable[float]],
- c0: Union[float, Iterable[float]],
- cf: Union[float, Iterable[float]],
- cw: Union[float, Iterable[float]],
- min_thresh: Union[float, Iterable[float]],
- slope: Union[float, Iterable[float]] = 3.5,
- lower_asymptote: Union[float, Iterable[float]] = 0.01,
- lapse_rate: Union[float, Iterable[float]] = 0.01,
- scale: str = 'log10') -> np.ndarray:
+def csf(
+ *,
+ contrast: Union[float, Iterable[float]],
+ spatial_freq: Union[float, Iterable[float]],
+ temporal_freq: Union[float, Iterable[float]],
+ c0: Union[float, Iterable[float]],
+ cf: Union[float, Iterable[float]],
+ cw: Union[float, Iterable[float]],
+ min_thresh: Union[float, Iterable[float]],
+ slope: Union[float, Iterable[float]] = 3.5,
+ lower_asymptote: Union[float, Iterable[float]] = 0.01,
+ lapse_rate: Union[float, Iterable[float]] = 0.01,
+ scale: str = "log10",
+) -> np.ndarray:
"""
The spatio-temporal contrast sensitivity function.
@@ -154,26 +164,30 @@ def csf(*,
# slope, lower_asymptote, lapse_rate,
# indexing='ij', sparse=True)
- x = xr.DataArray(data=contrast, dims=['contrast'],
- coords=dict(contrast=contrast))
- f = xr.DataArray(data=spatial_freq, dims=['spatial_freq'],
- coords=dict(spatial_freq=spatial_freq))
- w = xr.DataArray(data=temporal_freq, dims=['temporal_freq'],
- coords=dict(temporal_freq=temporal_freq))
- c0_ = xr.DataArray(data=c0, dims=['c0'],
- coords=dict(c0=c0))
- cf_ = xr.DataArray(data=cf, dims=['cf'],
- coords=dict(cf=cf))
- cw_ = xr.DataArray(data=cw, dims=['cw'],
- coords=dict(cw=cw))
- min_t = xr.DataArray(data=min_thresh, dims=['min_thresh'],
- coords=dict(min_thresh=min_thresh))
- beta = xr.DataArray(data=slope, dims=['slope'],
- coords=dict(slope=slope))
- gamma = xr.DataArray(data=lower_asymptote, dims=['lower_asymptote'],
- coords=dict(lower_asymptote=lower_asymptote))
- delta = xr.DataArray(data=lapse_rate, dims=['lapse_rate'],
- coords=dict(lapse_rate=lapse_rate))
+ x = xr.DataArray(data=contrast, dims=["contrast"], coords=dict(contrast=contrast))
+ f = xr.DataArray(
+ data=spatial_freq, dims=["spatial_freq"], coords=dict(spatial_freq=spatial_freq)
+ )
+ w = xr.DataArray(
+ data=temporal_freq,
+ dims=["temporal_freq"],
+ coords=dict(temporal_freq=temporal_freq),
+ )
+ c0_ = xr.DataArray(data=c0, dims=["c0"], coords=dict(c0=c0))
+ cf_ = xr.DataArray(data=cf, dims=["cf"], coords=dict(cf=cf))
+ cw_ = xr.DataArray(data=cw, dims=["cw"], coords=dict(cw=cw))
+ min_t = xr.DataArray(
+ data=min_thresh, dims=["min_thresh"], coords=dict(min_thresh=min_thresh)
+ )
+ beta = xr.DataArray(data=slope, dims=["slope"], coords=dict(slope=slope))
+ gamma = xr.DataArray(
+ data=lower_asymptote,
+ dims=["lower_asymptote"],
+ coords=dict(lower_asymptote=lower_asymptote),
+ )
+ delta = xr.DataArray(
+ data=lapse_rate, dims=["lapse_rate"], coords=dict(lapse_rate=lapse_rate)
+ )
t = np.maximum(min_t, c0_ + cf_ * f + cw_ * w)
@@ -184,25 +198,27 @@ def csf(*,
# lapse_rate=lapse_rate,
# scale=scale)
- if scale == 'linear':
- p = 1 - delta - (1 - gamma - delta) * np.exp(-(x / t)**beta)
- elif scale == 'log10':
- p = 1 - delta - (1 - gamma - delta) * np.exp(-10 ** (beta * (x - t)))
- elif scale == 'dB':
- p = 1 - delta - (1 - gamma - delta) * np.exp(-10 ** (beta * (x - t) / 20))
+ if scale == "linear":
+ p = 1 - delta - (1 - gamma - delta) * np.exp(-((x / t) ** beta))
+ elif scale == "log10":
+ p = 1 - delta - (1 - gamma - delta) * np.exp(-(10 ** (beta * (x - t))))
+ elif scale == "dB":
+ p = 1 - delta - (1 - gamma - delta) * np.exp(-(10 ** (beta * (x - t) / 20)))
else:
- raise ValueError('Invalid scale specified.')
+ raise ValueError("Invalid scale specified.")
return p
-def norm_cdf(*,
- intensity: Union[float, Iterable[float]],
- mean: Union[float, Iterable[float]],
- sd: Union[float, Iterable[float]],
- lower_asymptote: Union[float, Iterable[float]] = 0.01,
- lapse_rate: Union[float, Iterable[float]] = 0.01,
- scale: str = 'linear'):
+def norm_cdf(
+ *,
+ intensity: Union[float, Iterable[float]],
+ mean: Union[float, Iterable[float]],
+ sd: Union[float, Iterable[float]],
+ lower_asymptote: Union[float, Iterable[float]] = 0.01,
+ lapse_rate: Union[float, Iterable[float]] = 0.01,
+ scale: str = "linear",
+):
"""
The cumulate normal distribution.
@@ -219,9 +235,11 @@ def norm_cdf(*,
-------
"""
- if scale != 'linear':
- msg = ('Currently, only linear stimulus scaling is supported for this '
- 'psychometric function.')
+ if scale != "linear":
+ msg = (
+ "Currently, only linear stimulus scaling is supported for this "
+ "psychometric function."
+ )
raise ValueError(msg)
intensity = np.atleast_1d(intensity)
@@ -230,16 +248,19 @@ def norm_cdf(*,
lower_asymptote = np.atleast_1d(lower_asymptote)
lapse_rate = np.atleast_1d(lapse_rate)
- x = xr.DataArray(data=intensity, dims=['intensity'],
- coords=dict(intensity=intensity))
- mu = xr.DataArray(data=mean, dims=['mean'],
- coords=dict(mean=mean))
- sd_ = xr.DataArray(data=sd, dims=['sd'],
- coords=dict(sd=sd))
- gamma = xr.DataArray(data=lower_asymptote, dims=['lower_asymptote'],
- coords=dict(lower_asymptote=lower_asymptote))
- delta = xr.DataArray(data=lapse_rate, dims=['lapse_rate'],
- coords=dict(lapse_rate=lapse_rate))
+ x = xr.DataArray(
+ data=intensity, dims=["intensity"], coords=dict(intensity=intensity)
+ )
+ mu = xr.DataArray(data=mean, dims=["mean"], coords=dict(mean=mean))
+ sd_ = xr.DataArray(data=sd, dims=["sd"], coords=dict(sd=sd))
+ gamma = xr.DataArray(
+ data=lower_asymptote,
+ dims=["lower_asymptote"],
+ coords=dict(lower_asymptote=lower_asymptote),
+ )
+ delta = xr.DataArray(
+ data=lapse_rate, dims=["lapse_rate"], coords=dict(lapse_rate=lapse_rate)
+ )
# x, mu, sd_, delta = np.meshgrid(intensity,
# mean,
@@ -256,18 +277,20 @@ def norm_cdf(*,
def _mu_func(x, mu, sd_, gamma, delta):
norm = scipy.stats.norm(loc=mu, scale=sd_)
- return delta + (1 - gamma - delta) * norm.cdf(x)
+ return gamma + (1 - gamma - delta) * norm.cdf(x)
p = xr.apply_ufunc(_mu_func, x, mu, sd_, gamma, delta)
return p
-def norm_cdf_2(*,
- intensity: Union[float, Iterable[float]],
- mean: Union[float, Iterable[float]],
- sd: Union[float, Iterable[float]],
- lapse_rate: Union[float, Iterable[float]] = 0.01,
- scale: str = 'linear'):
+def norm_cdf_2(
+ *,
+ intensity: Union[float, Iterable[float]],
+ mean: Union[float, Iterable[float]],
+ sd: Union[float, Iterable[float]],
+ lapse_rate: Union[float, Iterable[float]] = 0.01,
+ scale: str = "linear",
+):
"""
The cumulative normal distribution with lapse rate equal to lower
asymptote.
@@ -284,9 +307,11 @@ def norm_cdf_2(*,
-------
"""
- if scale != 'linear':
- msg = ('Currently, only linear stimulus scaling is supported for this '
- 'psychometric function.')
+ if scale != "linear":
+ msg = (
+ "Currently, only linear stimulus scaling is supported for this "
+ "psychometric function."
+ )
raise ValueError(msg)
intensity = np.atleast_1d(intensity)
@@ -294,18 +319,170 @@ def norm_cdf_2(*,
sd = np.atleast_1d(sd)
lapse_rate = np.atleast_1d(lapse_rate)
- x = xr.DataArray(data=intensity, dims=['intensity'],
- coords=dict(intensity=intensity))
- mu = xr.DataArray(data=mean, dims=['mean'],
- coords=dict(mean=mean))
- sd_ = xr.DataArray(data=sd, dims=['sd'],
- coords=dict(sd=sd))
- delta = xr.DataArray(data=lapse_rate, dims=['lapse_rate'],
- coords=dict(lapse_rate=lapse_rate))
+ x = xr.DataArray(
+ data=intensity, dims=["intensity"], coords=dict(intensity=intensity)
+ )
+ mu = xr.DataArray(data=mean, dims=["mean"], coords=dict(mean=mean))
+ sd_ = xr.DataArray(data=sd, dims=["sd"], coords=dict(sd=sd))
+ delta = xr.DataArray(
+ data=lapse_rate, dims=["lapse_rate"], coords=dict(lapse_rate=lapse_rate)
+ )
def _mu_func(x, mu, sd_, delta):
norm = scipy.stats.norm(loc=mu, scale=sd_)
- return delta + (1 - 2*delta) * norm.cdf(x)
+ return delta + (1 - 2 * delta) * norm.cdf(x)
p = xr.apply_ufunc(_mu_func, x, mu, sd_, delta)
return p
+
+
+def scaling_function(
+ *,
+ x: Union[ArrayLike, float],
+ m: float,
+ mag_min: float = 0,
+ mag_max: float = 1,
+ t: float,
+ q: float,
+) -> ArrayLike:
+ """
+ The scaling function.
+
+ Parameters
+ ----------
+ x
+ This pyhysical stimulus magnitude(s).
+ m
+ The maximum value of the subjective scale.
+ mag_min
+ The minimum value of the physical stimulus magnitude.
+ mag_max
+ The maximum value of the physical stimulus magnitude.
+ t
+ The threshold value (physical stimulus magnitude at which the
+ participant starts to perceive the stimulus).
+ q
+ The power exponent.
+
+ Returns
+ -------
+ result
+ The subjectively perceived intensities corresponding to the physical
+ stimulus magnitudes.
+ """
+ # x = np.atleast_1d(x)
+ # m = np.atleast_1d(m)
+ # mag_min = np.atleast_1d(mag_min)
+ # mag_max = np.atleast_1d(mag_max)
+ # t = np.atleast_1d(t)
+ # q = np.atleast_1d(q)
+ #
+ # assert len(mag_min) == len(mag_max) == 1
+
+ nom = np.maximum(mag_min, x - t)
+ denom = mag_max - t
+
+ result = m * (nom / denom) ** q
+ return result
+
+
+def thurstone_scaling_function(
+ *,
+ physical_magnitudes_stim_1: Union[ArrayLike, float],
+ physical_magnitudes_stim_2: Union[ArrayLike, float],
+ threshold: Union[ArrayLike, float],
+ power: Union[ArrayLike, float],
+ perceptual_scale_max: Union[ArrayLike, float],
+) -> ArrayLike:
+ """
+ The Thurstone scaling function.
+
+ Parameters
+ ----------
+ physical_magnitudes_stim_1, physical_magnitudes_stim_2
+ This pyhysical stimulus magnitudes the participant is asked to
+ compare. All possible pairings will be generated automatically.
+ The values in each array must be unique.
+ threshold
+ The threshold value (physical stimulus magnitude at which the
+ participant starts to perceive the stimulus).
+ power
+ The power exponent.
+ perceptual_scale_max
+ The maximum value of the subjective perceptual scale (in JND / S.D.).
+
+ Returns
+ -------
+ """
+ physical_magnitudes_stim_1 = np.atleast_1d(physical_magnitudes_stim_1)
+ physical_magnitudes_stim_2 = np.atleast_1d(physical_magnitudes_stim_2)
+ threshold = np.atleast_1d(threshold)
+ power = np.atleast_1d(power)
+ perceptual_scale_max = np.atleast_1d(perceptual_scale_max)
+
+ # assert np.allclose(physical_magnitudes_stim_1, physical_magnitudes_stim_2)
+ # mag_min = x1.min()
+ # mag_max = x2.max()
+
+ # assert len(physical_magnitudes_stim_1) == len(physical_magnitudes_stim_2)
+ # assert np.allclose(physical_magnitudes_stim_1.min(), physical_magnitudes_stim_2.min())
+ # assert np.allclose(physical_magnitudes_stim_1.max(), physical_magnitudes_stim_2.max())
+
+ if not np.array_equal(
+ np.unique(physical_magnitudes_stim_1), np.sort(physical_magnitudes_stim_1)
+ ):
+ raise ValueError(f"Values in physical_magnitudes_stim_1 must be unique.")
+ if not np.array_equal(
+ np.unique(physical_magnitudes_stim_2), np.sort(physical_magnitudes_stim_2)
+ ):
+ raise ValueError(f"Values in physical_magnitudes_stim_2 must be unique.")
+
+ # mag_min = np.min([physical_magnitudes_stim_1, physical_magnitudes_stim_2])
+ mag_min = 0
+ mag_max = np.hstack([
+ physical_magnitudes_stim_1,
+ physical_magnitudes_stim_2
+ ]).max()
+
+ physical_magnitudes_stim_1 = xr.DataArray(
+ data=physical_magnitudes_stim_1,
+ dims=["physical_magnitude_stim_1"],
+ coords={"physical_magnitude_stim_1": physical_magnitudes_stim_1},
+ )
+ physical_magnitudes_stim_2 = xr.DataArray(
+ data=physical_magnitudes_stim_2,
+ dims=["physical_magnitude_stim_2"],
+ coords={"physical_magnitude_stim_2": physical_magnitudes_stim_2},
+ )
+ threshold = xr.DataArray(
+ data=threshold, dims=["threshold"], coords={"threshold": threshold}
+ )
+ power = xr.DataArray(data=power, dims=["power"], coords={"power": power})
+ perceptual_scale_max = xr.DataArray(
+ data=perceptual_scale_max,
+ dims=["perceptual_scale_max"],
+ coords={"perceptual_scale_max": perceptual_scale_max},
+ )
+
+ scale_x1 = scaling_function(
+ x=physical_magnitudes_stim_1,
+ m=perceptual_scale_max,
+ mag_min=mag_min,
+ mag_max=mag_max,
+ t=threshold,
+ q=power,
+ )
+ scale_x2 = scaling_function(
+ x=physical_magnitudes_stim_2,
+ m=perceptual_scale_max,
+ mag_min=mag_min,
+ mag_max=mag_max,
+ t=threshold,
+ q=power,
+ )
+
+ def _mu_func(scale_x1, scale_x2):
+ return scipy.stats.norm.cdf((scale_x1 - scale_x2) / np.sqrt(2))
+
+ result = xr.apply_ufunc(_mu_func, scale_x1, scale_x2)
+ return result
=====================================
questplus/qp.py
=====================================
@@ -1,23 +1,27 @@
-from typing import Optional, Sequence
-import xarray as xr
+from typing import Optional, Sequence, Literal
+from copy import deepcopy
+
import numpy as np
+import xarray as xr
import json_tricks
-from copy import deepcopy
from questplus import psychometric_function
class QuestPlus:
- def __init__(self, *,
- stim_domain: dict,
- param_domain: dict,
- outcome_domain: dict,
- prior: Optional[dict] = None,
- func: str,
- stim_scale: str,
- stim_selection_method: str = 'min_entropy',
- stim_selection_options: Optional[dict] = None,
- param_estimation_method: str = 'mean'):
+ def __init__(
+ self,
+ *,
+ stim_domain: dict,
+ param_domain: dict,
+ outcome_domain: dict,
+ prior: Optional[dict] = None,
+ func: Literal["weibull", "csf", "norm_cdf", "norm_cdf_2", "thurstone_scaling"],
+ stim_scale: Optional[Literal["log10", "dB", "linear"]],
+ stim_selection_method: str = "min_entropy",
+ stim_selection_options: Optional[dict] = None,
+ param_estimation_method: str = "mean",
+ ):
"""
A QUEST+ staircase procedure.
@@ -46,13 +50,11 @@ class QuestPlus:
A-priori probabilities of parameter values.
func
- The psychometric function whose parameters to estimate. Currently
- supported are the Weibull function, `weibull`, and the spatio-
- temporal contrast sensitivity function, `csf`.
+ The psychometric function whose parameters to estimate.
stim_scale
- The scale on which the stimuli are provided. Currently supported
- are the decadic logarithm, `log10`; and decibels, `dB`.
+ The scale on which the stimuli are provided. Has no effect for the
+ Thurstonian scaling function.
stim_selection_method
How to select the next stimulus. `min_entropy` picks the stimulus
@@ -77,6 +79,12 @@ class QuestPlus:
the posterior distribution).
"""
+ if func == "thurstone_scaling" and stim_scale is not None:
+ raise ValueError(
+ "The Thurstonian scaling function cannot be used with "
+ "a stim_scale parameter."
+ )
+
self.func = func
self.stim_scale = stim_scale
self.stim_domain = self._ensure_ndarray(stim_domain)
@@ -89,28 +97,34 @@ class QuestPlus:
self.stim_selection = stim_selection_method
- if self.stim_selection == 'min_n_entropy':
- from ._constants import (DEFAULT_N, DEFAULT_RANDOM_SEED,
- DEFAULT_MAX_CONSECUTIVE_REPS)
+ if self.stim_selection == "min_n_entropy":
+ from ._constants import (
+ DEFAULT_N,
+ DEFAULT_RANDOM_SEED,
+ DEFAULT_MAX_CONSECUTIVE_REPS,
+ )
if stim_selection_options is None:
self.stim_selection_options = dict(
n=DEFAULT_N,
max_consecutive_reps=DEFAULT_MAX_CONSECUTIVE_REPS,
- random_seed=DEFAULT_RANDOM_SEED)
+ random_seed=DEFAULT_RANDOM_SEED,
+ )
else:
self.stim_selection_options = stim_selection_options.copy()
- if 'n' not in stim_selection_options:
- self.stim_selection_options['n'] = DEFAULT_N
- if 'max_consecutive_reps' not in stim_selection_options:
- self.stim_selection_options['max_consecutive_reps'] = DEFAULT_MAX_CONSECUTIVE_REPS
- if 'random_seed' not in stim_selection_options:
- self.stim_selection_options['random_seed'] = DEFAULT_RANDOM_SEED
+ if "n" not in stim_selection_options:
+ self.stim_selection_options["n"] = DEFAULT_N
+ if "max_consecutive_reps" not in stim_selection_options:
+ self.stim_selection_options[
+ "max_consecutive_reps"
+ ] = DEFAULT_MAX_CONSECUTIVE_REPS
+ if "random_seed" not in stim_selection_options:
+ self.stim_selection_options["random_seed"] = DEFAULT_RANDOM_SEED
del DEFAULT_N, DEFAULT_MAX_CONSECUTIVE_REPS, DEFAULT_RANDOM_SEED
- seed = self.stim_selection_options['random_seed']
+ seed = self.stim_selection_options["random_seed"]
self._rng = np.random.RandomState(seed=seed)
del seed
else:
@@ -131,8 +145,7 @@ class QuestPlus:
return x
- def _gen_prior(self, *,
- prior: dict) -> xr.DataArray:
+ def _gen_prior(self, *, prior: dict) -> xr.DataArray:
"""
Raises
------
@@ -147,11 +160,13 @@ class QuestPlus:
# Uninformative prior.
prior = np.ones([len(x) for x in self.param_domain.values()])
elif set(prior_orig.keys()) - set(self.param_domain.keys()):
- msg = (f'Mismatch between specified parameter domain and supplied '
- f'prior.\n'
- f'You specified priors for the following parameters that '
- f'do not appear in the parameter domain: '
- f'{set(prior_orig.keys()) - set(self.param_domain.keys())}')
+ msg = (
+ f"Mismatch between specified parameter domain and supplied "
+ f"prior.\n"
+ f"You specified priors for the following parameters that "
+ f"do not appear in the parameter domain: "
+ f"{set(prior_orig.keys()) - set(self.param_domain.keys())}"
+ )
raise ValueError(msg)
elif set(self.param_domain.keys()) - set(prior_orig.keys()):
# The user specified prior probabilities for only a subset
@@ -163,28 +178,30 @@ class QuestPlus:
prior_vals = np.atleast_1d(prior_orig[param_name])
else:
prior_vals = np.ones(len(param_vals))
-
+
grid_dims.append(prior_vals)
- prior_grid = np.meshgrid(*grid_dims,
- sparse=True, indexing='ij')
- prior = np.prod(prior_grid)
+ prior_grid = np.meshgrid(*grid_dims, sparse=True, indexing="ij")
+ prior = np.prod(
+ np.array(prior_grid, dtype="object") # avoid warning re "ragged" array
+ )
else:
# A "proper" prior was specified (i.e., prior probabilities for
# all parameters.)
- prior_grid = np.meshgrid(*list(prior_orig.values()),
- sparse=True, indexing='ij')
- prior = np.prod(prior_grid)
+ prior_grid = np.meshgrid(
+ *list(prior_orig.values()), sparse=True, indexing="ij"
+ )
+ prior = np.prod(
+ np.array(prior_grid, dtype="object") # avoid warning re "ragged" array
+ )
# Normalize.
prior /= prior.sum()
# Create the prior object we are actually going to use.
- dims = *self.param_domain.keys(),
+ dims = (*self.param_domain.keys(),)
coords = dict(**self.param_domain)
- prior_ = xr.DataArray(data=prior,
- dims=dims,
- coords=coords)
+ prior_ = xr.DataArray(data=prior, dims=dims, coords=coords)
return prior_
@@ -192,43 +209,54 @@ class QuestPlus:
outcome_dim_name = list(self.outcome_domain.keys())[0]
outcome_values = list(self.outcome_domain.values())[0]
- if self.func in ['weibull', 'csf', 'norm_cdf', 'norm_cdf_2']:
- if self.func == 'weibull':
- f = psychometric_function.weibull
- elif self.func == 'csf':
- f = psychometric_function.csf
- elif self.func == 'norm_cdf':
- f = psychometric_function.norm_cdf
- else:
- f = psychometric_function.norm_cdf_2
-
- prop_correct = f(**self.stim_domain,
- **self.param_domain,
- scale=self.stim_scale)
-
- prop_incorrect = 1 - prop_correct
-
- # Now this is a bit awkward. We concatenate the psychometric
- # functions for the different responses. To do that, we first have
- # to add an additional dimension.
- # TODO: There's got to be a neater way to do this?!
- corr_resp_dim = {outcome_dim_name: [outcome_values[0]]}
- inccorr_resp_dim = {outcome_dim_name: [outcome_values[1]]}
-
- prop_correct = prop_correct.expand_dims(corr_resp_dim)
- prop_incorrect = prop_incorrect.expand_dims(inccorr_resp_dim)
-
- pf_values = xr.concat([prop_correct, prop_incorrect],
- dim=outcome_dim_name,
- coords=self.outcome_domain)
+ if self.func not in [
+ "weibull",
+ "csf",
+ "norm_cdf",
+ "norm_cdf_2",
+ "thurstone_scaling",
+ ]:
+ raise ValueError(
+ f"Unknown psychometric function name specified: {self.func}"
+ )
+
+ if self.func == "weibull":
+ f = psychometric_function.weibull
+ elif self.func == "csf":
+ f = psychometric_function.csf
+ elif self.func == "norm_cdf":
+ f = psychometric_function.norm_cdf
+ elif self.func == "norm_cdf_2":
+ f = psychometric_function.norm_cdf_2
+ elif self.func == "thurstone_scaling":
+ f = psychometric_function.thurstone_scaling_function
+
+ if self.func == "thurstone_scaling":
+ prop_correct = f(**self.stim_domain, **self.param_domain)
else:
- raise ValueError('Unknown psychometric function name specified.')
-
+ prop_correct = f(
+ **self.stim_domain, **self.param_domain, scale=self.stim_scale
+ )
+ prop_incorrect = 1 - prop_correct
+
+ # Now this is a bit awkward. We concatenate the psychometric
+ # functions for the different responses. To do that, we first have
+ # to add an additional dimension.
+ # TODO: There's got to be a neater way to do this?!
+ corr_resp_dim = {outcome_dim_name: [outcome_values[0]]}
+ inccorr_resp_dim = {outcome_dim_name: [outcome_values[1]]}
+
+ prop_correct = prop_correct.expand_dims(corr_resp_dim)
+ prop_incorrect = prop_incorrect.expand_dims(inccorr_resp_dim)
+
+ pf_values = xr.concat(
+ [prop_correct, prop_incorrect],
+ dim=outcome_dim_name,
+ coords=self.outcome_domain,
+ )
return pf_values
- def update(self, *,
- stim: dict,
- outcome: dict) -> None:
+ def update(self, *, stim: dict, outcome: dict) -> None:
"""
Inform QUEST+ about a newly gathered measurement outcome for a given
stimulus parameter set, and update the posterior accordingly.
@@ -242,8 +270,7 @@ class QuestPlus:
The observed outcome.
"""
- likelihood = (self.likelihoods
- .sel(**stim, **outcome))
+ likelihood = self.likelihoods.sel(**stim, **outcome)
self.posterior = self.posterior * likelihood
self.posterior /= self.posterior.sum()
@@ -268,25 +295,37 @@ class QuestPlus:
new_posterior /= pk
# Entropies.
- # Note that np.log(0) returns nan; xr.DataArray.sum() has special
- # handling for this case.
- H = -((new_posterior * np.log(new_posterior))
- .sum(dim=self.param_domain.keys()))
+ #
+ # Note:
+ # - np.log(0) returns -inf (division by zero)
+ # - the multiplcation of new_posterior with -inf values generates
+ # NaN's
+ # - xr.DataArray.sum() has special handling for NaN's.
+ #
+ # NumPy also emits a warning, which we suppress here.
+ with np.errstate(divide="ignore"):
+ H = -(
+ (new_posterior * np.log(new_posterior)).sum(
+ dim=self.param_domain.keys()
+ )
+ )
# Expected entropies for all possible stimulus parameters.
EH = (pk * H).sum(dim=list(self.outcome_domain.keys()))
- if self.stim_selection == 'min_entropy':
- # Get coordinates of stimulus properties that minimize entropy.
- index = np.unravel_index(EH.argmin(), EH.shape)
- coords = EH[index].coords
- stim = {stim_property: stim_val.item()
- for stim_property, stim_val in coords.items()}
+ if self.stim_selection == "min_entropy":
+ # Get the stimulus properties that minimize entropy.
+ indices = EH.argmin(dim=...)
+ stim = dict()
+ for stim_property, index in indices.items():
+ stim_val = EH[stim_property][index].item()
+ stim[stim_property] = stim_val
+
self.entropy = EH.min().item()
- elif self.stim_selection == 'min_n_entropy':
+ elif self.stim_selection == "min_n_entropy":
# Number of stimuli to include (the n stimuli that yield the lowest
# entropies)
- n_stim = self.stim_selection_options['n']
+ n_stim = self.stim_selection_options["n"]
indices = np.unravel_index(EH.argsort(), EH.shape)[0]
indices = indices[:n_stim]
@@ -296,21 +335,24 @@ class QuestPlus:
# (stimulus parameters).
candidate_index = self._rng.choice(indices)
coords = EH[candidate_index].coords
- stim = {stim_property: stim_val.item()
- for stim_property, stim_val in coords.items()}
+ stim = {
+ stim_property: stim_val.item()
+ for stim_property, stim_val in coords.items()
+ }
- max_reps = self.stim_selection_options['max_consecutive_reps']
+ max_reps = self.stim_selection_options["max_consecutive_reps"]
if len(self.stim_history) < 2:
break
- elif all([stim == prev_stim
- for prev_stim in self.stim_history[-max_reps:]]):
+ elif all(
+ [stim == prev_stim for prev_stim in self.stim_history[-max_reps:]]
+ ):
# Shuffle again.
continue
else:
break
else:
- raise ValueError('Unknown stim_selection supplied.')
+ raise ValueError("Unknown stim_selection supplied.")
return stim
@@ -332,18 +374,18 @@ class QuestPlus:
params = list(self.param_domain.keys())
params.remove(param_name)
- if method == 'mean':
- param_estimates[param_name] = ((self.posterior.sum(dim=params) *
- self.param_domain[param_name])
- .sum()
- .item())
- elif method == 'mode':
- index = np.unravel_index(self.posterior.argmax(),
- self.posterior.shape)
- coords = self.posterior[index].coords
+ if method == "mean":
+ param_estimates[param_name] = (
+ (self.posterior.sum(dim=params) * self.param_domain[param_name])
+ .sum()
+ .item()
+ )
+ elif method == "mode":
+ indices = self.posterior.argmax(dim=...)
+ coords = self.posterior[indices]
param_estimates[param_name] = coords[param_name].item()
else:
- raise ValueError('Unknown method parameter.')
+ raise ValueError("Unknown method parameter.")
return param_estimates
@@ -361,9 +403,9 @@ class QuestPlus:
for param_name in self.param_domain.keys():
marginalized_out_params = list(self.param_domain.keys())
marginalized_out_params.remove(param_name)
- marginal_posterior[param_name] = (self.posterior
- .sum(dim=marginalized_out_params)
- .values)
+ marginal_posterior[param_name] = self.posterior.sum(
+ dim=marginalized_out_params
+ ).values
return marginal_posterior
@@ -435,18 +477,21 @@ class QuestPlus:
return False
for param_name in self.param_domain.keys():
- if not np.array_equal(self.param_domain[param_name],
- other.param_domain[param_name]):
+ if not np.array_equal(
+ self.param_domain[param_name], other.param_domain[param_name]
+ ):
return False
for stim_property in self.stim_domain.keys():
- if not np.array_equal(self.stim_domain[stim_property],
- other.stim_domain[stim_property]):
+ if not np.array_equal(
+ self.stim_domain[stim_property], other.stim_domain[stim_property]
+ ):
return False
for outcome_name in self.outcome_domain.keys():
- if not np.array_equal(self.outcome_domain[outcome_name],
- other.outcome_domain[outcome_name]):
+ if not np.array_equal(
+ self.outcome_domain[outcome_name], other.outcome_domain[outcome_name]
+ ):
return False
if self.stim_selection != other.stim_selection:
@@ -474,83 +519,92 @@ class QuestPlus:
class QuestPlusWeibull(QuestPlus):
- def __init__(self, *,
- intensities: Sequence,
- thresholds: Sequence,
- slopes: Sequence,
- lower_asymptotes: Sequence,
- lapse_rates: Sequence,
- prior: Optional[dict] = None,
- responses: Sequence = ('Yes', 'No'),
- stim_scale: str = 'log10',
- stim_selection_method: str = 'min_entropy',
- stim_selection_options: Optional[dict] = None,
- param_estimation_method: str = 'mean'):
- super().__init__(stim_domain=dict(intensity=intensities),
- param_domain=dict(threshold=thresholds,
- slope=slopes,
- lower_asymptote=lower_asymptotes,
- lapse_rate=lapse_rates),
- outcome_domain=dict(response=responses),
- prior=prior,
- stim_scale=stim_scale,
- stim_selection_method=stim_selection_method,
- stim_selection_options=stim_selection_options,
- param_estimation_method=param_estimation_method,
- func='weibull')
+ def __init__(
+ self,
+ *,
+ intensities: Sequence,
+ thresholds: Sequence,
+ slopes: Sequence,
+ lower_asymptotes: Sequence,
+ lapse_rates: Sequence,
+ prior: Optional[dict] = None,
+ responses: Sequence = ("Yes", "No"),
+ stim_scale: str = "log10",
+ stim_selection_method: str = "min_entropy",
+ stim_selection_options: Optional[dict] = None,
+ param_estimation_method: str = "mean",
+ ):
+ """QUEST+ using the Weibull distribution function.
+
+ This is a convenience class that wraps `QuestPlus`.
+ """
+ super().__init__(
+ stim_domain=dict(intensity=intensities),
+ param_domain=dict(
+ threshold=thresholds,
+ slope=slopes,
+ lower_asymptote=lower_asymptotes,
+ lapse_rate=lapse_rates,
+ ),
+ outcome_domain=dict(response=responses),
+ prior=prior,
+ stim_scale=stim_scale,
+ stim_selection_method=stim_selection_method,
+ stim_selection_options=stim_selection_options,
+ param_estimation_method=param_estimation_method,
+ func="weibull",
+ )
@property
def intensities(self) -> np.ndarray:
"""
Stimulus intensity or contrast domain.
"""
- return self.stim_domain['intensity']
+ return self.stim_domain["intensity"]
@property
def thresholds(self) -> np.ndarray:
"""
The threshold parameter domain.
"""
- return self.param_domain['threshold']
+ return self.param_domain["threshold"]
@property
def slopes(self) -> np.ndarray:
"""
The slope parameter domain.
"""
- return self.param_domain['slope']
+ return self.param_domain["slope"]
@property
def lower_asymptotes(self) -> np.ndarray:
"""
The lower asymptote parameter domain.
"""
- return self.param_domain['lower_asymptote']
+ return self.param_domain["lower_asymptote"]
@property
def lapse_rates(self) -> np.ndarray:
"""
The lapse rate parameter domain.
"""
- return self.param_domain['lapse_rate']
+ return self.param_domain["lapse_rate"]
@property
def responses(self) -> np.ndarray:
"""
The response (outcome) domain.
"""
- return self.outcome_domain['response']
+ return self.outcome_domain["response"]
@property
def next_intensity(self) -> float:
"""
The intensity or contrast to present next.
"""
- return super().next_stim['intensity']
+ return super().next_stim["intensity"]
- def update(self, *,
- intensity: float,
- response: str) -> None:
+ def update(self, *, intensity: float, response: str) -> None:
"""
Inform QUEST+ about a newly gathered measurement outcome for a given
stimulus intensity or contrast, and update the posterior accordingly.
@@ -564,5 +618,101 @@ class QuestPlusWeibull(QuestPlus):
The observed response.
"""
- super().update(stim=dict(intensity=intensity),
- outcome=dict(response=response))
+ super().update(stim=dict(intensity=intensity), outcome=dict(response=response))
+
+
+class QuestPlusThurstone(QuestPlus):
+ def __init__(
+ self,
+ *,
+ physical_magnitudes_stim_1: Sequence,
+ physical_magnitudes_stim_2: Sequence,
+ thresholds: Sequence,
+ powers: Sequence,
+ perceptual_scale_maxs: Sequence,
+ prior: Optional[dict] = None,
+ responses: Sequence = ("First", "Second"),
+ stim_selection_method: str = "min_entropy",
+ stim_selection_options: Optional[dict] = None,
+ param_estimation_method: str = "mean",
+ ):
+ """QUEST+ for Thurstonian scaling.
+
+ This is a convenience class that wraps `QuestPlus`.
+ """
+ super().__init__(
+ stim_domain={
+ "physical_magnitudes_stim_1": physical_magnitudes_stim_1,
+ "physical_magnitudes_stim_2": physical_magnitudes_stim_2,
+ },
+ param_domain={
+ "threshold": thresholds,
+ "power": powers,
+ "perceptual_scale_max": perceptual_scale_maxs,
+ },
+ outcome_domain={"response": responses},
+ prior=prior,
+ stim_scale=None,
+ stim_selection_method=stim_selection_method,
+ stim_selection_options=stim_selection_options,
+ param_estimation_method=param_estimation_method,
+ func="thurstone_scaling",
+ )
+
+ @property
+ def physical_magnitudes_stim_1(self) -> np.ndarray:
+ """
+ Physical magnitudes of the first stimulus.
+ """
+ return self.stim_domain["physical_magnitudes_stim_1"]
+
+ @property
+ def physical_magnitudes_stim_2(self) -> np.ndarray:
+ """
+ Physical magnitudes of the second stimulus.
+ """
+ return self.stim_domain["physical_magnitudes_stim_2"]
+
+ @property
+ def thresholds(self) -> np.ndarray:
+ """
+ The threshold parameter domain.
+ """
+ return self.param_domain["threshold"]
+
+ @property
+ def powers(self) -> np.ndarray:
+ """
+ The power parameter domain.
+ """
+ return self.param_domain["power"]
+
+ @property
+ def perceptual_scale_maxss(self) -> np.ndarray:
+ """
+ The "maximum value of the subjective perceptual scale" parameter domain.
+ """
+ return self.param_domain["perceptual_scale_max"]
+
+ @property
+ def responses(self) -> np.ndarray:
+ """
+ The response (outcome) domain.
+ """
+ return self.outcome_domain["response"]
+
+ def update(self, *, stim: dict, response: str) -> None:
+ """
+ Inform QUEST+ about a newly gathered measurement outcome for a given
+ stimulus parameter set, and update the posterior accordingly.
+
+ Parameters
+ ----------
+ stim
+ The stimulus that was used to generate the given outcome.
+
+ outcome
+ The observed outcome.
+
+ """
+ super().update(stim=stim, outcome=dict(response=response))
=====================================
questplus/tests/test_qp.py
=====================================
@@ -1,7 +1,7 @@
import pytest
import scipy.stats
import numpy as np
-from questplus.qp import QuestPlus, QuestPlusWeibull
+from questplus.qp import QuestPlus, QuestPlusWeibull, QuestPlusThurstone
from questplus import _constants
@@ -373,6 +373,82 @@ def test_spatial_contrast_sensitivity():
expected_mode_cf)
+def test_thurstone_scaling():
+ """
+ Watson 2017, Example 6:
+ "Thurstone scaling {2, 3, 2}"
+ """
+ stim_magnitudes = np.arange(0, 1+0.1, 0.1)
+ perceptual_scale_maxs = np.arange(1, 10+1)
+ thresholds = np.arange(0, 0.9+0.1, 0.1)
+ powers = np.arange(0.1, 1+0.1, 0.1)
+
+ # Due to differences in rounding, the order of stimuli (1 or 2) is swapped on some trials
+ # compared to the paper. We therefore have to swap the example response as well.
+ #
+ # We're only testing the first 22 trials here.
+ responses = ['Second'] * 6
+ responses.extend(['Second']) # rounding difference
+ responses.extend(['Second'] * 13)
+ responses.extend(['Second']) # rounding difference
+ responses.extend(['First'])
+
+ expected_stims = [
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.7},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.6},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.5},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.4},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.0},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.4},
+ {'physical_magnitude_stim_1': 0.0, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.5, 'physical_magnitude_stim_2': 1.0},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.5, 'physical_magnitude_stim_2': 1.0},
+ {'physical_magnitude_stim_1': 0.5, 'physical_magnitude_stim_2': 1.0},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.5, 'physical_magnitude_stim_2': 1.0},
+ {'physical_magnitude_stim_1': 0.6, 'physical_magnitude_stim_2': 1.0},
+ {'physical_magnitude_stim_1': 0.2, 'physical_magnitude_stim_2': 0.3},
+ {'physical_magnitude_stim_1': 0.6, 'physical_magnitude_stim_2': 1.0},
+ ]
+
+ qp = QuestPlusThurstone(
+ physical_magnitudes_stim_1=stim_magnitudes,
+ physical_magnitudes_stim_2=stim_magnitudes,
+ thresholds=thresholds,
+ powers=powers,
+ perceptual_scale_maxs=perceptual_scale_maxs
+ )
+
+ for trial_idx, x in enumerate(zip(expected_stims, responses)):
+ expected_stim, response = x
+
+ expected_stim_1 = expected_stim['physical_magnitude_stim_1']
+ expected_stim_2 = expected_stim['physical_magnitude_stim_2']
+
+ next_stim_1 = qp.next_stim['physical_magnitude_stim_1']
+ next_stim_2 = qp.next_stim['physical_magnitude_stim_2']
+
+ if trial_idx in (6, 20):
+ # Rounding errors make the algorithm behave differently on different platforms.
+ if (
+ expected_stim_1 == next_stim_2 and
+ expected_stim_2 == next_stim_1
+ ):
+ expected_stim_1, expected_stim_2 = expected_stim_2, expected_stim_1
+ response = 'First' if response == 'Second' else 'Second'
+
+ assert np.isclose(next_stim_1, expected_stim_1)
+ assert np.isclose(next_stim_2, expected_stim_2)
+ qp.update(stim=qp.next_stim, response=response)
+
+
def test_weibull():
threshold = np.arange(-40, 0 + 1)
slope, guess, lapse = 3.5, 0.5, 0.02
=====================================
questplus/utils.py
=====================================
@@ -3,12 +3,14 @@ import numpy as np
from questplus import psychometric_function
-def simulate_response(*,
- func: str = 'weibull',
- stimulus: dict,
- params: dict,
- response_domain: Sequence = ('Correct', 'Incorrect'),
- stim_scale: str = 'log10') -> Union[float, str]:
+def simulate_response(
+ *,
+ func: str = "weibull",
+ stimulus: dict,
+ params: dict,
+ response_domain: Sequence = ("Correct", "Incorrect"),
+ stim_scale: str = "log10",
+) -> Union[float, str]:
"""
Simulate an observer with the given psychometric function parameters.
@@ -36,14 +38,14 @@ def simulate_response(*,
A simulated response for the given stimulus.
"""
- if func == 'weibull':
+ if func == "weibull":
f = psychometric_function.weibull
- p_correct = f(intensity=stimulus['intensity'],
- **params, scale=stim_scale).squeeze()
+ p_correct = f(
+ intensity=stimulus["intensity"], **params, scale=stim_scale
+ ).squeeze()
- response = np.random.choice(response_domain,
- p=[p_correct, 1-p_correct])
+ response = np.random.choice(response_domain, p=[p_correct, 1 - p_correct])
else:
- raise ValueError('Invalid function specified.')
+ raise ValueError("Invalid function specified.")
return response
=====================================
setup.cfg deleted
=====================================
@@ -1,38 +0,0 @@
-[metadata]
-name = questplus
-author = Richard Höchenberger <richard.hoechenberger at gmail.com>
-author_email = richard.hoechenberger at gmail.com
-url = https://github.com/hoechenberger/questplus
-project_urls =
- Source Code = https://github.com/hoechenberger/questplus
- Bug Tracker = https://github.com/hoechenberger/questplus/issues
-license = GPL v3
-license_file = LICENSE
-description = A QUEST+ implementation in Python.
-long_description = file: README.md
-long_description_content_type = text/markdown
-classifiers =
- Intended Audience :: Science/Research
- Programming Language :: Python
- Programming Language :: Python :: 3
- Programming Language :: Python :: 3.6
- Programming Language :: Python :: 3.7
- Programming Language :: Python :: 3.8
-
-[options]
-python_requires = >=3.6
-install_requires =
- numpy
- scipy
- xarray
- json_tricks
-
-[bdist_wheel]
-universal = 1
-
-[versioneer]
-VCS = git
-style = pep440
-versionfile_source = questplus/_version.py
-versionfile_build = questplus/_version.py
-tag_prefix = ''
=====================================
setup.py deleted
=====================================
@@ -1,15 +0,0 @@
-import sys
-import versioneer
-
-
-try:
- from setuptools import setup, find_packages
-except ImportError:
- raise sys.exit('Could not import setuptools.')
-
-
-setup(
- version=versioneer.get_version(),
- cmdclass=versioneer.get_cmdclass(),
- packages=find_packages()
-)
=====================================
versioneer.py deleted
=====================================
@@ -1,1822 +0,0 @@
-
-# Version: 0.18
-
-"""The Versioneer - like a rocketeer, but for versions.
-
-The Versioneer
-==============
-
-* like a rocketeer, but for versions!
-* https://github.com/warner/python-versioneer
-* Brian Warner
-* License: Public Domain
-* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
-* [![Latest Version]
-(https://pypip.in/version/versioneer/badge.svg?style=flat)
-](https://pypi.python.org/pypi/versioneer/)
-* [![Build Status]
-(https://travis-ci.org/warner/python-versioneer.png?branch=master)
-](https://travis-ci.org/warner/python-versioneer)
-
-This is a tool for managing a recorded version number in distutils-based
-python projects. The goal is to remove the tedious and error-prone "update
-the embedded version string" step from your release process. Making a new
-release should be as easy as recording a new tag in your version-control
-system, and maybe making new tarballs.
-
-
-## Quick Install
-
-* `pip install versioneer` to somewhere to your $PATH
-* add a `[versioneer]` section to your setup.cfg (see below)
-* run `versioneer install` in your source tree, commit the results
-
-## Version Identifiers
-
-Source trees come from a variety of places:
-
-* a version-control system checkout (mostly used by developers)
-* a nightly tarball, produced by build automation
-* a snapshot tarball, produced by a web-based VCS browser, like github's
- "tarball from tag" feature
-* a release tarball, produced by "setup.py sdist", distributed through PyPI
-
-Within each source tree, the version identifier (either a string or a number,
-this tool is format-agnostic) can come from a variety of places:
-
-* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows
- about recent "tags" and an absolute revision-id
-* the name of the directory into which the tarball was unpacked
-* an expanded VCS keyword ($Id$, etc)
-* a `_version.py` created by some earlier build step
-
-For released software, the version identifier is closely related to a VCS
-tag. Some projects use tag names that include more than just the version
-string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool
-needs to strip the tag prefix to extract the version identifier. For
-unreleased software (between tags), the version identifier should provide
-enough information to help developers recreate the same tree, while also
-giving them an idea of roughly how old the tree is (after version 1.2, before
-version 1.3). Many VCS systems can report a description that captures this,
-for example `git describe --tags --dirty --always` reports things like
-"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the
-0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has
-uncommitted changes.
-
-The version identifier is used for multiple purposes:
-
-* to allow the module to self-identify its version: `myproject.__version__`
-* to choose a name and prefix for a 'setup.py sdist' tarball
-
-## Theory of Operation
-
-Versioneer works by adding a special `_version.py` file into your source
-tree, where your `__init__.py` can import it. This `_version.py` knows how to
-dynamically ask the VCS tool for version information at import time.
-
-`_version.py` also contains `$Revision$` markers, and the installation
-process marks `_version.py` to have this marker rewritten with a tag name
-during the `git archive` command. As a result, generated tarballs will
-contain enough information to get the proper version.
-
-To allow `setup.py` to compute a version too, a `versioneer.py` is added to
-the top level of your source tree, next to `setup.py` and the `setup.cfg`
-that configures it. This overrides several distutils/setuptools commands to
-compute the version when invoked, and changes `setup.py build` and `setup.py
-sdist` to replace `_version.py` with a small static file that contains just
-the generated version data.
-
-## Installation
-
-See [INSTALL.md](./INSTALL.md) for detailed installation instructions.
-
-## Version-String Flavors
-
-Code which uses Versioneer can learn about its version string at runtime by
-importing `_version` from your main `__init__.py` file and running the
-`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can
-import the top-level `versioneer.py` and run `get_versions()`.
-
-Both functions return a dictionary with different flavors of version
-information:
-
-* `['version']`: A condensed version string, rendered using the selected
- style. This is the most commonly used value for the project's version
- string. The default "pep440" style yields strings like `0.11`,
- `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section
- below for alternative styles.
-
-* `['full-revisionid']`: detailed revision identifier. For Git, this is the
- full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac".
-
-* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the
- commit date in ISO 8601 format. This will be None if the date is not
- available.
-
-* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that
- this is only accurate if run in a VCS checkout, otherwise it is likely to
- be False or None
-
-* `['error']`: if the version string could not be computed, this will be set
- to a string describing the problem, otherwise it will be None. It may be
- useful to throw an exception in setup.py if this is set, to avoid e.g.
- creating tarballs with a version string of "unknown".
-
-Some variants are more useful than others. Including `full-revisionid` in a
-bug report should allow developers to reconstruct the exact code being tested
-(or indicate the presence of local changes that should be shared with the
-developers). `version` is suitable for display in an "about" box or a CLI
-`--version` output: it can be easily compared against release notes and lists
-of bugs fixed in various releases.
-
-The installer adds the following text to your `__init__.py` to place a basic
-version in `YOURPROJECT.__version__`:
-
- from ._version import get_versions
- __version__ = get_versions()['version']
- del get_versions
-
-## Styles
-
-The setup.cfg `style=` configuration controls how the VCS information is
-rendered into a version string.
-
-The default style, "pep440", produces a PEP440-compliant string, equal to the
-un-prefixed tag name for actual releases, and containing an additional "local
-version" section with more detail for in-between builds. For Git, this is
-TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags
---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the
-tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and
-that this commit is two revisions ("+2") beyond the "0.11" tag. For released
-software (exactly equal to a known tag), the identifier will only contain the
-stripped tag, e.g. "0.11".
-
-Other styles are available. See [details.md](details.md) in the Versioneer
-source tree for descriptions.
-
-## Debugging
-
-Versioneer tries to avoid fatal errors: if something goes wrong, it will tend
-to return a version of "0+unknown". To investigate the problem, run `setup.py
-version`, which will run the version-lookup code in a verbose mode, and will
-display the full contents of `get_versions()` (including the `error` string,
-which may help identify what went wrong).
-
-## Known Limitations
-
-Some situations are known to cause problems for Versioneer. This details the
-most significant ones. More can be found on Github
-[issues page](https://github.com/warner/python-versioneer/issues).
-
-### Subprojects
-
-Versioneer has limited support for source trees in which `setup.py` is not in
-the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are
-two common reasons why `setup.py` might not be in the root:
-
-* Source trees which contain multiple subprojects, such as
- [Buildbot](https://github.com/buildbot/buildbot), which contains both
- "master" and "slave" subprojects, each with their own `setup.py`,
- `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI
- distributions (and upload multiple independently-installable tarballs).
-* Source trees whose main purpose is to contain a C library, but which also
- provide bindings to Python (and perhaps other langauges) in subdirectories.
-
-Versioneer will look for `.git` in parent directories, and most operations
-should get the right version string. However `pip` and `setuptools` have bugs
-and implementation details which frequently cause `pip install .` from a
-subproject directory to fail to find a correct version string (so it usually
-defaults to `0+unknown`).
-
-`pip install --editable .` should work correctly. `setup.py install` might
-work too.
-
-Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in
-some later version.
-
-[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking
-this issue. The discussion in
-[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the
-issue from the Versioneer side in more detail.
-[pip PR#3176](https://github.com/pypa/pip/pull/3176) and
-[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve
-pip to let Versioneer work correctly.
-
-Versioneer-0.16 and earlier only looked for a `.git` directory next to the
-`setup.cfg`, so subprojects were completely unsupported with those releases.
-
-### Editable installs with setuptools <= 18.5
-
-`setup.py develop` and `pip install --editable .` allow you to install a
-project into a virtualenv once, then continue editing the source code (and
-test) without re-installing after every change.
-
-"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a
-convenient way to specify executable scripts that should be installed along
-with the python package.
-
-These both work as expected when using modern setuptools. When using
-setuptools-18.5 or earlier, however, certain operations will cause
-`pkg_resources.DistributionNotFound` errors when running the entrypoint
-script, which must be resolved by re-installing the package. This happens
-when the install happens with one version, then the egg_info data is
-regenerated while a different version is checked out. Many setup.py commands
-cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into
-a different virtualenv), so this can be surprising.
-
-[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes
-this one, but upgrading to a newer version of setuptools should probably
-resolve it.
-
-### Unicode version strings
-
-While Versioneer works (and is continually tested) with both Python 2 and
-Python 3, it is not entirely consistent with bytes-vs-unicode distinctions.
-Newer releases probably generate unicode version strings on py2. It's not
-clear that this is wrong, but it may be surprising for applications when then
-write these strings to a network connection or include them in bytes-oriented
-APIs like cryptographic checksums.
-
-[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates
-this question.
-
-
-## Updating Versioneer
-
-To upgrade your project to a new release of Versioneer, do the following:
-
-* install the new Versioneer (`pip install -U versioneer` or equivalent)
-* edit `setup.cfg`, if necessary, to include any new configuration settings
- indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details.
-* re-run `versioneer install` in your source tree, to replace
- `SRC/_version.py`
-* commit any changed files
-
-## Future Directions
-
-This tool is designed to make it easily extended to other version-control
-systems: all VCS-specific components are in separate directories like
-src/git/ . The top-level `versioneer.py` script is assembled from these
-components by running make-versioneer.py . In the future, make-versioneer.py
-will take a VCS name as an argument, and will construct a version of
-`versioneer.py` that is specific to the given VCS. It might also take the
-configuration arguments that are currently provided manually during
-installation by editing setup.py . Alternatively, it might go the other
-direction and include code from all supported VCS systems, reducing the
-number of intermediate scripts.
-
-
-## License
-
-To make Versioneer easier to embed, all its code is dedicated to the public
-domain. The `_version.py` that it creates is also in the public domain.
-Specifically, both are released under the Creative Commons "Public Domain
-Dedication" license (CC0-1.0), as described in
-https://creativecommons.org/publicdomain/zero/1.0/ .
-
-"""
-
-from __future__ import print_function
-try:
- import configparser
-except ImportError:
- import ConfigParser as configparser
-import errno
-import json
-import os
-import re
-import subprocess
-import sys
-
-
-class VersioneerConfig:
- """Container for Versioneer configuration parameters."""
-
-
-def get_root():
- """Get the project root directory.
-
- We require that all commands are run from the project root, i.e. the
- directory that contains setup.py, setup.cfg, and versioneer.py .
- """
- root = os.path.realpath(os.path.abspath(os.getcwd()))
- setup_py = os.path.join(root, "setup.py")
- versioneer_py = os.path.join(root, "versioneer.py")
- if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
- # allow 'python path/to/setup.py COMMAND'
- root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0])))
- setup_py = os.path.join(root, "setup.py")
- versioneer_py = os.path.join(root, "versioneer.py")
- if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)):
- err = ("Versioneer was unable to run the project root directory. "
- "Versioneer requires setup.py to be executed from "
- "its immediate directory (like 'python setup.py COMMAND'), "
- "or in a way that lets it use sys.argv[0] to find the root "
- "(like 'python path/to/setup.py COMMAND').")
- raise VersioneerBadRootError(err)
- try:
- # Certain runtime workflows (setup.py install/develop in a setuptools
- # tree) execute all dependencies in a single python process, so
- # "versioneer" may be imported multiple times, and python's shared
- # module-import table will cache the first one. So we can't use
- # os.path.dirname(__file__), as that will find whichever
- # versioneer.py was first imported, even in later projects.
- me = os.path.realpath(os.path.abspath(__file__))
- me_dir = os.path.normcase(os.path.splitext(me)[0])
- vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0])
- if me_dir != vsr_dir:
- print("Warning: build in %s is using versioneer.py from %s"
- % (os.path.dirname(me), versioneer_py))
- except NameError:
- pass
- return root
-
-
-def get_config_from_root(root):
- """Read the project setup.cfg file to determine Versioneer config."""
- # This might raise EnvironmentError (if setup.cfg is missing), or
- # configparser.NoSectionError (if it lacks a [versioneer] section), or
- # configparser.NoOptionError (if it lacks "VCS="). See the docstring at
- # the top of versioneer.py for instructions on writing your setup.cfg .
- setup_cfg = os.path.join(root, "setup.cfg")
- parser = configparser.SafeConfigParser()
- with open(setup_cfg, "r") as f:
- parser.readfp(f)
- VCS = parser.get("versioneer", "VCS") # mandatory
-
- def get(parser, name):
- if parser.has_option("versioneer", name):
- return parser.get("versioneer", name)
- return None
- cfg = VersioneerConfig()
- cfg.VCS = VCS
- cfg.style = get(parser, "style") or ""
- cfg.versionfile_source = get(parser, "versionfile_source")
- cfg.versionfile_build = get(parser, "versionfile_build")
- cfg.tag_prefix = get(parser, "tag_prefix")
- if cfg.tag_prefix in ("''", '""'):
- cfg.tag_prefix = ""
- cfg.parentdir_prefix = get(parser, "parentdir_prefix")
- cfg.verbose = get(parser, "verbose")
- return cfg
-
-
-class NotThisMethod(Exception):
- """Exception raised if a method is not valid for the current scenario."""
-
-
-# these dictionaries contain VCS-specific tools
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
-
-def register_vcs_handler(vcs, method): # decorator
- """Decorator to mark a method as the handler for a particular VCS."""
- def decorate(f):
- """Store f in HANDLERS[vcs][method]."""
- if vcs not in HANDLERS:
- HANDLERS[vcs] = {}
- HANDLERS[vcs][method] = f
- return f
- return decorate
-
-
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
- env=None):
- """Call the given command(s)."""
- assert isinstance(commands, list)
- p = None
- for c in commands:
- try:
- dispcmd = str([c] + args)
- # remember shell=False, so use git.cmd on windows, not just git
- p = subprocess.Popen([c] + args, cwd=cwd, env=env,
- stdout=subprocess.PIPE,
- stderr=(subprocess.PIPE if hide_stderr
- else None))
- break
- except EnvironmentError:
- e = sys.exc_info()[1]
- if e.errno == errno.ENOENT:
- continue
- if verbose:
- print("unable to run %s" % dispcmd)
- print(e)
- return None, None
- else:
- if verbose:
- print("unable to find command, tried %s" % (commands,))
- return None, None
- stdout = p.communicate()[0].strip()
- if sys.version_info[0] >= 3:
- stdout = stdout.decode()
- if p.returncode != 0:
- if verbose:
- print("unable to run %s (error)" % dispcmd)
- print("stdout was %s" % stdout)
- return None, p.returncode
- return stdout, p.returncode
-
-
-LONG_VERSION_PY['git'] = '''
-# This file helps to compute a version number in source trees obtained from
-# git-archive tarball (such as those provided by githubs download-from-tag
-# feature). Distribution tarballs (built by setup.py sdist) and build
-# directories (produced by setup.py build) will contain a much shorter file
-# that just contains the computed version number.
-
-# This file is released into the public domain. Generated by
-# versioneer-0.18 (https://github.com/warner/python-versioneer)
-
-"""Git implementation of _version.py."""
-
-import errno
-import os
-import re
-import subprocess
-import sys
-
-
-def get_keywords():
- """Get the keywords needed to look up the version information."""
- # these strings will be replaced by git during git-archive.
- # setup.py/versioneer.py will grep for the variable names, so they must
- # each be defined on a line of their own. _version.py will just call
- # get_keywords().
- git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s"
- git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s"
- git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s"
- keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
- return keywords
-
-
-class VersioneerConfig:
- """Container for Versioneer configuration parameters."""
-
-
-def get_config():
- """Create, populate and return the VersioneerConfig() object."""
- # these strings are filled in when 'setup.py versioneer' creates
- # _version.py
- cfg = VersioneerConfig()
- cfg.VCS = "git"
- cfg.style = "%(STYLE)s"
- cfg.tag_prefix = "%(TAG_PREFIX)s"
- cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s"
- cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s"
- cfg.verbose = False
- return cfg
-
-
-class NotThisMethod(Exception):
- """Exception raised if a method is not valid for the current scenario."""
-
-
-LONG_VERSION_PY = {}
-HANDLERS = {}
-
-
-def register_vcs_handler(vcs, method): # decorator
- """Decorator to mark a method as the handler for a particular VCS."""
- def decorate(f):
- """Store f in HANDLERS[vcs][method]."""
- if vcs not in HANDLERS:
- HANDLERS[vcs] = {}
- HANDLERS[vcs][method] = f
- return f
- return decorate
-
-
-def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False,
- env=None):
- """Call the given command(s)."""
- assert isinstance(commands, list)
- p = None
- for c in commands:
- try:
- dispcmd = str([c] + args)
- # remember shell=False, so use git.cmd on windows, not just git
- p = subprocess.Popen([c] + args, cwd=cwd, env=env,
- stdout=subprocess.PIPE,
- stderr=(subprocess.PIPE if hide_stderr
- else None))
- break
- except EnvironmentError:
- e = sys.exc_info()[1]
- if e.errno == errno.ENOENT:
- continue
- if verbose:
- print("unable to run %%s" %% dispcmd)
- print(e)
- return None, None
- else:
- if verbose:
- print("unable to find command, tried %%s" %% (commands,))
- return None, None
- stdout = p.communicate()[0].strip()
- if sys.version_info[0] >= 3:
- stdout = stdout.decode()
- if p.returncode != 0:
- if verbose:
- print("unable to run %%s (error)" %% dispcmd)
- print("stdout was %%s" %% stdout)
- return None, p.returncode
- return stdout, p.returncode
-
-
-def versions_from_parentdir(parentdir_prefix, root, verbose):
- """Try to determine the version from the parent directory name.
-
- Source tarballs conventionally unpack into a directory that includes both
- the project name and a version string. We will also support searching up
- two directory levels for an appropriately named parent directory
- """
- rootdirs = []
-
- for i in range(3):
- dirname = os.path.basename(root)
- if dirname.startswith(parentdir_prefix):
- return {"version": dirname[len(parentdir_prefix):],
- "full-revisionid": None,
- "dirty": False, "error": None, "date": None}
- else:
- rootdirs.append(root)
- root = os.path.dirname(root) # up a level
-
- if verbose:
- print("Tried directories %%s but none started with prefix %%s" %%
- (str(rootdirs), parentdir_prefix))
- raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
- at register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
- """Extract version information from the given file."""
- # the code embedded in _version.py can just fetch the value of these
- # keywords. When used from setup.py, we don't want to import _version.py,
- # so we do it with a regexp instead. This function is not used from
- # _version.py.
- keywords = {}
- try:
- f = open(versionfile_abs, "r")
- for line in f.readlines():
- if line.strip().startswith("git_refnames ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["refnames"] = mo.group(1)
- if line.strip().startswith("git_full ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["full"] = mo.group(1)
- if line.strip().startswith("git_date ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["date"] = mo.group(1)
- f.close()
- except EnvironmentError:
- pass
- return keywords
-
-
- at register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
- """Get version information from git keywords."""
- if not keywords:
- raise NotThisMethod("no keywords at all, weird")
- date = keywords.get("date")
- if date is not None:
- # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant
- # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601
- # -like" string, which we must then edit to make compliant), because
- # it's been around since git-1.5.3, and it's too difficult to
- # discover which version we're using, or to work around using an
- # older one.
- date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
- refnames = keywords["refnames"].strip()
- if refnames.startswith("$Format"):
- if verbose:
- print("keywords are unexpanded, not using")
- raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
- refs = set([r.strip() for r in refnames.strip("()").split(",")])
- # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
- # just "foo-1.0". If we see a "tag: " prefix, prefer those.
- TAG = "tag: "
- tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
- if not tags:
- # Either we're using git < 1.8.3, or there really are no tags. We use
- # a heuristic: assume all version tags have a digit. The old git %%d
- # expansion behaves like git log --decorate=short and strips out the
- # refs/heads/ and refs/tags/ prefixes that would let us distinguish
- # between branches and tags. By ignoring refnames without digits, we
- # filter out many common branch names like "release" and
- # "stabilization", as well as "HEAD" and "master".
- tags = set([r for r in refs if re.search(r'\d', r)])
- if verbose:
- print("discarding '%%s', no digits" %% ",".join(refs - tags))
- if verbose:
- print("likely tags: %%s" %% ",".join(sorted(tags)))
- for ref in sorted(tags):
- # sorting will prefer e.g. "2.0" over "2.0rc1"
- if ref.startswith(tag_prefix):
- r = ref[len(tag_prefix):]
- if verbose:
- print("picking %%s" %% r)
- return {"version": r,
- "full-revisionid": keywords["full"].strip(),
- "dirty": False, "error": None,
- "date": date}
- # no suitable tags, so version is "0+unknown", but full hex is still there
- if verbose:
- print("no suitable tags, using unknown + full revision id")
- return {"version": "0+unknown",
- "full-revisionid": keywords["full"].strip(),
- "dirty": False, "error": "no suitable tags", "date": None}
-
-
- at register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
- """Get version from 'git describe' in the root of the source tree.
-
- This only gets called if the git-archive 'subst' keywords were *not*
- expanded, and _version.py hasn't already been rewritten with a short
- version string, meaning we're inside a checked out source tree.
- """
- GITS = ["git"]
- if sys.platform == "win32":
- GITS = ["git.cmd", "git.exe"]
-
- out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
- hide_stderr=True)
- if rc != 0:
- if verbose:
- print("Directory %%s not under git control" %% root)
- raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
- # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
- # if there isn't one, this yields HEX[-dirty] (no NUM)
- describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
- "--always", "--long",
- "--match", "%%s*" %% tag_prefix],
- cwd=root)
- # --long was added in git-1.5.5
- if describe_out is None:
- raise NotThisMethod("'git describe' failed")
- describe_out = describe_out.strip()
- full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
- if full_out is None:
- raise NotThisMethod("'git rev-parse' failed")
- full_out = full_out.strip()
-
- pieces = {}
- pieces["long"] = full_out
- pieces["short"] = full_out[:7] # maybe improved later
- pieces["error"] = None
-
- # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
- # TAG might have hyphens.
- git_describe = describe_out
-
- # look for -dirty suffix
- dirty = git_describe.endswith("-dirty")
- pieces["dirty"] = dirty
- if dirty:
- git_describe = git_describe[:git_describe.rindex("-dirty")]
-
- # now we have TAG-NUM-gHEX or HEX
-
- if "-" in git_describe:
- # TAG-NUM-gHEX
- mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
- if not mo:
- # unparseable. Maybe git-describe is misbehaving?
- pieces["error"] = ("unable to parse git-describe output: '%%s'"
- %% describe_out)
- return pieces
-
- # tag
- full_tag = mo.group(1)
- if not full_tag.startswith(tag_prefix):
- if verbose:
- fmt = "tag '%%s' doesn't start with prefix '%%s'"
- print(fmt %% (full_tag, tag_prefix))
- pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'"
- %% (full_tag, tag_prefix))
- return pieces
- pieces["closest-tag"] = full_tag[len(tag_prefix):]
-
- # distance: number of commits since tag
- pieces["distance"] = int(mo.group(2))
-
- # commit: short hex revision ID
- pieces["short"] = mo.group(3)
-
- else:
- # HEX: no tags
- pieces["closest-tag"] = None
- count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
- cwd=root)
- pieces["distance"] = int(count_out) # total number of commits
-
- # commit date: see ISO-8601 comment in git_versions_from_keywords()
- date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"],
- cwd=root)[0].strip()
- pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-
- return pieces
-
-
-def plus_or_dot(pieces):
- """Return a + if we don't already have one, else return a ."""
- if "+" in pieces.get("closest-tag", ""):
- return "."
- return "+"
-
-
-def render_pep440(pieces):
- """Build up version string, with post-release "local version identifier".
-
- Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
- get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
- Exceptions:
- 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += plus_or_dot(pieces)
- rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"])
- if pieces["dirty"]:
- rendered += ".dirty"
- else:
- # exception #1
- rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"],
- pieces["short"])
- if pieces["dirty"]:
- rendered += ".dirty"
- return rendered
-
-
-def render_pep440_pre(pieces):
- """TAG[.post.devDISTANCE] -- No -dirty.
-
- Exceptions:
- 1: no tags. 0.post.devDISTANCE
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"]:
- rendered += ".post.dev%%d" %% pieces["distance"]
- else:
- # exception #1
- rendered = "0.post.dev%%d" %% pieces["distance"]
- return rendered
-
-
-def render_pep440_post(pieces):
- """TAG[.postDISTANCE[.dev0]+gHEX] .
-
- The ".dev0" means dirty. Note that .dev0 sorts backwards
- (a dirty tree will appear "older" than the corresponding clean one),
- but you shouldn't be releasing software with -dirty anyways.
-
- Exceptions:
- 1: no tags. 0.postDISTANCE[.dev0]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += ".post%%d" %% pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- rendered += plus_or_dot(pieces)
- rendered += "g%%s" %% pieces["short"]
- else:
- # exception #1
- rendered = "0.post%%d" %% pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- rendered += "+g%%s" %% pieces["short"]
- return rendered
-
-
-def render_pep440_old(pieces):
- """TAG[.postDISTANCE[.dev0]] .
-
- The ".dev0" means dirty.
-
- Eexceptions:
- 1: no tags. 0.postDISTANCE[.dev0]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += ".post%%d" %% pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- else:
- # exception #1
- rendered = "0.post%%d" %% pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- return rendered
-
-
-def render_git_describe(pieces):
- """TAG[-DISTANCE-gHEX][-dirty].
-
- Like 'git describe --tags --dirty --always'.
-
- Exceptions:
- 1: no tags. HEX[-dirty] (note: no 'g' prefix)
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"]:
- rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
- else:
- # exception #1
- rendered = pieces["short"]
- if pieces["dirty"]:
- rendered += "-dirty"
- return rendered
-
-
-def render_git_describe_long(pieces):
- """TAG-DISTANCE-gHEX[-dirty].
-
- Like 'git describe --tags --dirty --always -long'.
- The distance/hash is unconditional.
-
- Exceptions:
- 1: no tags. HEX[-dirty] (note: no 'g' prefix)
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"])
- else:
- # exception #1
- rendered = pieces["short"]
- if pieces["dirty"]:
- rendered += "-dirty"
- return rendered
-
-
-def render(pieces, style):
- """Render the given version pieces into the requested style."""
- if pieces["error"]:
- return {"version": "unknown",
- "full-revisionid": pieces.get("long"),
- "dirty": None,
- "error": pieces["error"],
- "date": None}
-
- if not style or style == "default":
- style = "pep440" # the default
-
- if style == "pep440":
- rendered = render_pep440(pieces)
- elif style == "pep440-pre":
- rendered = render_pep440_pre(pieces)
- elif style == "pep440-post":
- rendered = render_pep440_post(pieces)
- elif style == "pep440-old":
- rendered = render_pep440_old(pieces)
- elif style == "git-describe":
- rendered = render_git_describe(pieces)
- elif style == "git-describe-long":
- rendered = render_git_describe_long(pieces)
- else:
- raise ValueError("unknown style '%%s'" %% style)
-
- return {"version": rendered, "full-revisionid": pieces["long"],
- "dirty": pieces["dirty"], "error": None,
- "date": pieces.get("date")}
-
-
-def get_versions():
- """Get version information or return default if unable to do so."""
- # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have
- # __file__, we can work backwards from there to the root. Some
- # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which
- # case we can only use expanded keywords.
-
- cfg = get_config()
- verbose = cfg.verbose
-
- try:
- return git_versions_from_keywords(get_keywords(), cfg.tag_prefix,
- verbose)
- except NotThisMethod:
- pass
-
- try:
- root = os.path.realpath(__file__)
- # versionfile_source is the relative path from the top of the source
- # tree (where the .git directory might live) to this file. Invert
- # this to find the root from __file__.
- for i in cfg.versionfile_source.split('/'):
- root = os.path.dirname(root)
- except NameError:
- return {"version": "0+unknown", "full-revisionid": None,
- "dirty": None,
- "error": "unable to find root of source tree",
- "date": None}
-
- try:
- pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose)
- return render(pieces, cfg.style)
- except NotThisMethod:
- pass
-
- try:
- if cfg.parentdir_prefix:
- return versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
- except NotThisMethod:
- pass
-
- return {"version": "0+unknown", "full-revisionid": None,
- "dirty": None,
- "error": "unable to compute version", "date": None}
-'''
-
-
- at register_vcs_handler("git", "get_keywords")
-def git_get_keywords(versionfile_abs):
- """Extract version information from the given file."""
- # the code embedded in _version.py can just fetch the value of these
- # keywords. When used from setup.py, we don't want to import _version.py,
- # so we do it with a regexp instead. This function is not used from
- # _version.py.
- keywords = {}
- try:
- f = open(versionfile_abs, "r")
- for line in f.readlines():
- if line.strip().startswith("git_refnames ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["refnames"] = mo.group(1)
- if line.strip().startswith("git_full ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["full"] = mo.group(1)
- if line.strip().startswith("git_date ="):
- mo = re.search(r'=\s*"(.*)"', line)
- if mo:
- keywords["date"] = mo.group(1)
- f.close()
- except EnvironmentError:
- pass
- return keywords
-
-
- at register_vcs_handler("git", "keywords")
-def git_versions_from_keywords(keywords, tag_prefix, verbose):
- """Get version information from git keywords."""
- if not keywords:
- raise NotThisMethod("no keywords at all, weird")
- date = keywords.get("date")
- if date is not None:
- # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant
- # datestamp. However we prefer "%ci" (which expands to an "ISO-8601
- # -like" string, which we must then edit to make compliant), because
- # it's been around since git-1.5.3, and it's too difficult to
- # discover which version we're using, or to work around using an
- # older one.
- date = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
- refnames = keywords["refnames"].strip()
- if refnames.startswith("$Format"):
- if verbose:
- print("keywords are unexpanded, not using")
- raise NotThisMethod("unexpanded keywords, not a git-archive tarball")
- refs = set([r.strip() for r in refnames.strip("()").split(",")])
- # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of
- # just "foo-1.0". If we see a "tag: " prefix, prefer those.
- TAG = "tag: "
- tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)])
- if not tags:
- # Either we're using git < 1.8.3, or there really are no tags. We use
- # a heuristic: assume all version tags have a digit. The old git %d
- # expansion behaves like git log --decorate=short and strips out the
- # refs/heads/ and refs/tags/ prefixes that would let us distinguish
- # between branches and tags. By ignoring refnames without digits, we
- # filter out many common branch names like "release" and
- # "stabilization", as well as "HEAD" and "master".
- tags = set([r for r in refs if re.search(r'\d', r)])
- if verbose:
- print("discarding '%s', no digits" % ",".join(refs - tags))
- if verbose:
- print("likely tags: %s" % ",".join(sorted(tags)))
- for ref in sorted(tags):
- # sorting will prefer e.g. "2.0" over "2.0rc1"
- if ref.startswith(tag_prefix):
- r = ref[len(tag_prefix):]
- if verbose:
- print("picking %s" % r)
- return {"version": r,
- "full-revisionid": keywords["full"].strip(),
- "dirty": False, "error": None,
- "date": date}
- # no suitable tags, so version is "0+unknown", but full hex is still there
- if verbose:
- print("no suitable tags, using unknown + full revision id")
- return {"version": "0+unknown",
- "full-revisionid": keywords["full"].strip(),
- "dirty": False, "error": "no suitable tags", "date": None}
-
-
- at register_vcs_handler("git", "pieces_from_vcs")
-def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command):
- """Get version from 'git describe' in the root of the source tree.
-
- This only gets called if the git-archive 'subst' keywords were *not*
- expanded, and _version.py hasn't already been rewritten with a short
- version string, meaning we're inside a checked out source tree.
- """
- GITS = ["git"]
- if sys.platform == "win32":
- GITS = ["git.cmd", "git.exe"]
-
- out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root,
- hide_stderr=True)
- if rc != 0:
- if verbose:
- print("Directory %s not under git control" % root)
- raise NotThisMethod("'git rev-parse --git-dir' returned error")
-
- # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty]
- # if there isn't one, this yields HEX[-dirty] (no NUM)
- describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty",
- "--always", "--long",
- "--match", "%s*" % tag_prefix],
- cwd=root)
- # --long was added in git-1.5.5
- if describe_out is None:
- raise NotThisMethod("'git describe' failed")
- describe_out = describe_out.strip()
- full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root)
- if full_out is None:
- raise NotThisMethod("'git rev-parse' failed")
- full_out = full_out.strip()
-
- pieces = {}
- pieces["long"] = full_out
- pieces["short"] = full_out[:7] # maybe improved later
- pieces["error"] = None
-
- # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty]
- # TAG might have hyphens.
- git_describe = describe_out
-
- # look for -dirty suffix
- dirty = git_describe.endswith("-dirty")
- pieces["dirty"] = dirty
- if dirty:
- git_describe = git_describe[:git_describe.rindex("-dirty")]
-
- # now we have TAG-NUM-gHEX or HEX
-
- if "-" in git_describe:
- # TAG-NUM-gHEX
- mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe)
- if not mo:
- # unparseable. Maybe git-describe is misbehaving?
- pieces["error"] = ("unable to parse git-describe output: '%s'"
- % describe_out)
- return pieces
-
- # tag
- full_tag = mo.group(1)
- if not full_tag.startswith(tag_prefix):
- if verbose:
- fmt = "tag '%s' doesn't start with prefix '%s'"
- print(fmt % (full_tag, tag_prefix))
- pieces["error"] = ("tag '%s' doesn't start with prefix '%s'"
- % (full_tag, tag_prefix))
- return pieces
- pieces["closest-tag"] = full_tag[len(tag_prefix):]
-
- # distance: number of commits since tag
- pieces["distance"] = int(mo.group(2))
-
- # commit: short hex revision ID
- pieces["short"] = mo.group(3)
-
- else:
- # HEX: no tags
- pieces["closest-tag"] = None
- count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"],
- cwd=root)
- pieces["distance"] = int(count_out) # total number of commits
-
- # commit date: see ISO-8601 comment in git_versions_from_keywords()
- date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"],
- cwd=root)[0].strip()
- pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1)
-
- return pieces
-
-
-def do_vcs_install(manifest_in, versionfile_source, ipy):
- """Git-specific installation logic for Versioneer.
-
- For Git, this means creating/changing .gitattributes to mark _version.py
- for export-subst keyword substitution.
- """
- GITS = ["git"]
- if sys.platform == "win32":
- GITS = ["git.cmd", "git.exe"]
- files = [manifest_in, versionfile_source]
- if ipy:
- files.append(ipy)
- try:
- me = __file__
- if me.endswith(".pyc") or me.endswith(".pyo"):
- me = os.path.splitext(me)[0] + ".py"
- versioneer_file = os.path.relpath(me)
- except NameError:
- versioneer_file = "versioneer.py"
- files.append(versioneer_file)
- present = False
- try:
- f = open(".gitattributes", "r")
- for line in f.readlines():
- if line.strip().startswith(versionfile_source):
- if "export-subst" in line.strip().split()[1:]:
- present = True
- f.close()
- except EnvironmentError:
- pass
- if not present:
- f = open(".gitattributes", "a+")
- f.write("%s export-subst\n" % versionfile_source)
- f.close()
- files.append(".gitattributes")
- run_command(GITS, ["add", "--"] + files)
-
-
-def versions_from_parentdir(parentdir_prefix, root, verbose):
- """Try to determine the version from the parent directory name.
-
- Source tarballs conventionally unpack into a directory that includes both
- the project name and a version string. We will also support searching up
- two directory levels for an appropriately named parent directory
- """
- rootdirs = []
-
- for i in range(3):
- dirname = os.path.basename(root)
- if dirname.startswith(parentdir_prefix):
- return {"version": dirname[len(parentdir_prefix):],
- "full-revisionid": None,
- "dirty": False, "error": None, "date": None}
- else:
- rootdirs.append(root)
- root = os.path.dirname(root) # up a level
-
- if verbose:
- print("Tried directories %s but none started with prefix %s" %
- (str(rootdirs), parentdir_prefix))
- raise NotThisMethod("rootdir doesn't start with parentdir_prefix")
-
-
-SHORT_VERSION_PY = """
-# This file was generated by 'versioneer.py' (0.18) from
-# revision-control system data, or from the parent directory name of an
-# unpacked source archive. Distribution tarballs contain a pre-generated copy
-# of this file.
-
-import json
-
-version_json = '''
-%s
-''' # END VERSION_JSON
-
-
-def get_versions():
- return json.loads(version_json)
-"""
-
-
-def versions_from_file(filename):
- """Try to determine the version from _version.py if present."""
- try:
- with open(filename) as f:
- contents = f.read()
- except EnvironmentError:
- raise NotThisMethod("unable to read _version.py")
- mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON",
- contents, re.M | re.S)
- if not mo:
- mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON",
- contents, re.M | re.S)
- if not mo:
- raise NotThisMethod("no version_json in _version.py")
- return json.loads(mo.group(1))
-
-
-def write_to_version_file(filename, versions):
- """Write the given version number to the given _version.py file."""
- os.unlink(filename)
- contents = json.dumps(versions, sort_keys=True,
- indent=1, separators=(",", ": "))
- with open(filename, "w") as f:
- f.write(SHORT_VERSION_PY % contents)
-
- print("set %s to '%s'" % (filename, versions["version"]))
-
-
-def plus_or_dot(pieces):
- """Return a + if we don't already have one, else return a ."""
- if "+" in pieces.get("closest-tag", ""):
- return "."
- return "+"
-
-
-def render_pep440(pieces):
- """Build up version string, with post-release "local version identifier".
-
- Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you
- get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty
-
- Exceptions:
- 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += plus_or_dot(pieces)
- rendered += "%d.g%s" % (pieces["distance"], pieces["short"])
- if pieces["dirty"]:
- rendered += ".dirty"
- else:
- # exception #1
- rendered = "0+untagged.%d.g%s" % (pieces["distance"],
- pieces["short"])
- if pieces["dirty"]:
- rendered += ".dirty"
- return rendered
-
-
-def render_pep440_pre(pieces):
- """TAG[.post.devDISTANCE] -- No -dirty.
-
- Exceptions:
- 1: no tags. 0.post.devDISTANCE
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"]:
- rendered += ".post.dev%d" % pieces["distance"]
- else:
- # exception #1
- rendered = "0.post.dev%d" % pieces["distance"]
- return rendered
-
-
-def render_pep440_post(pieces):
- """TAG[.postDISTANCE[.dev0]+gHEX] .
-
- The ".dev0" means dirty. Note that .dev0 sorts backwards
- (a dirty tree will appear "older" than the corresponding clean one),
- but you shouldn't be releasing software with -dirty anyways.
-
- Exceptions:
- 1: no tags. 0.postDISTANCE[.dev0]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += ".post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- rendered += plus_or_dot(pieces)
- rendered += "g%s" % pieces["short"]
- else:
- # exception #1
- rendered = "0.post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- rendered += "+g%s" % pieces["short"]
- return rendered
-
-
-def render_pep440_old(pieces):
- """TAG[.postDISTANCE[.dev0]] .
-
- The ".dev0" means dirty.
-
- Eexceptions:
- 1: no tags. 0.postDISTANCE[.dev0]
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"] or pieces["dirty"]:
- rendered += ".post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- else:
- # exception #1
- rendered = "0.post%d" % pieces["distance"]
- if pieces["dirty"]:
- rendered += ".dev0"
- return rendered
-
-
-def render_git_describe(pieces):
- """TAG[-DISTANCE-gHEX][-dirty].
-
- Like 'git describe --tags --dirty --always'.
-
- Exceptions:
- 1: no tags. HEX[-dirty] (note: no 'g' prefix)
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- if pieces["distance"]:
- rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
- else:
- # exception #1
- rendered = pieces["short"]
- if pieces["dirty"]:
- rendered += "-dirty"
- return rendered
-
-
-def render_git_describe_long(pieces):
- """TAG-DISTANCE-gHEX[-dirty].
-
- Like 'git describe --tags --dirty --always -long'.
- The distance/hash is unconditional.
-
- Exceptions:
- 1: no tags. HEX[-dirty] (note: no 'g' prefix)
- """
- if pieces["closest-tag"]:
- rendered = pieces["closest-tag"]
- rendered += "-%d-g%s" % (pieces["distance"], pieces["short"])
- else:
- # exception #1
- rendered = pieces["short"]
- if pieces["dirty"]:
- rendered += "-dirty"
- return rendered
-
-
-def render(pieces, style):
- """Render the given version pieces into the requested style."""
- if pieces["error"]:
- return {"version": "unknown",
- "full-revisionid": pieces.get("long"),
- "dirty": None,
- "error": pieces["error"],
- "date": None}
-
- if not style or style == "default":
- style = "pep440" # the default
-
- if style == "pep440":
- rendered = render_pep440(pieces)
- elif style == "pep440-pre":
- rendered = render_pep440_pre(pieces)
- elif style == "pep440-post":
- rendered = render_pep440_post(pieces)
- elif style == "pep440-old":
- rendered = render_pep440_old(pieces)
- elif style == "git-describe":
- rendered = render_git_describe(pieces)
- elif style == "git-describe-long":
- rendered = render_git_describe_long(pieces)
- else:
- raise ValueError("unknown style '%s'" % style)
-
- return {"version": rendered, "full-revisionid": pieces["long"],
- "dirty": pieces["dirty"], "error": None,
- "date": pieces.get("date")}
-
-
-class VersioneerBadRootError(Exception):
- """The project root directory is unknown or missing key files."""
-
-
-def get_versions(verbose=False):
- """Get the project version from whatever source is available.
-
- Returns dict with two keys: 'version' and 'full'.
- """
- if "versioneer" in sys.modules:
- # see the discussion in cmdclass.py:get_cmdclass()
- del sys.modules["versioneer"]
-
- root = get_root()
- cfg = get_config_from_root(root)
-
- assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg"
- handlers = HANDLERS.get(cfg.VCS)
- assert handlers, "unrecognized VCS '%s'" % cfg.VCS
- verbose = verbose or cfg.verbose
- assert cfg.versionfile_source is not None, \
- "please set versioneer.versionfile_source"
- assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix"
-
- versionfile_abs = os.path.join(root, cfg.versionfile_source)
-
- # extract version from first of: _version.py, VCS command (e.g. 'git
- # describe'), parentdir. This is meant to work for developers using a
- # source checkout, for users of a tarball created by 'setup.py sdist',
- # and for users of a tarball/zipball created by 'git archive' or github's
- # download-from-tag feature or the equivalent in other VCSes.
-
- get_keywords_f = handlers.get("get_keywords")
- from_keywords_f = handlers.get("keywords")
- if get_keywords_f and from_keywords_f:
- try:
- keywords = get_keywords_f(versionfile_abs)
- ver = from_keywords_f(keywords, cfg.tag_prefix, verbose)
- if verbose:
- print("got version from expanded keyword %s" % ver)
- return ver
- except NotThisMethod:
- pass
-
- try:
- ver = versions_from_file(versionfile_abs)
- if verbose:
- print("got version from file %s %s" % (versionfile_abs, ver))
- return ver
- except NotThisMethod:
- pass
-
- from_vcs_f = handlers.get("pieces_from_vcs")
- if from_vcs_f:
- try:
- pieces = from_vcs_f(cfg.tag_prefix, root, verbose)
- ver = render(pieces, cfg.style)
- if verbose:
- print("got version from VCS %s" % ver)
- return ver
- except NotThisMethod:
- pass
-
- try:
- if cfg.parentdir_prefix:
- ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose)
- if verbose:
- print("got version from parentdir %s" % ver)
- return ver
- except NotThisMethod:
- pass
-
- if verbose:
- print("unable to compute version")
-
- return {"version": "0+unknown", "full-revisionid": None,
- "dirty": None, "error": "unable to compute version",
- "date": None}
-
-
-def get_version():
- """Get the short version string for this project."""
- return get_versions()["version"]
-
-
-def get_cmdclass():
- """Get the custom setuptools/distutils subclasses used by Versioneer."""
- if "versioneer" in sys.modules:
- del sys.modules["versioneer"]
- # this fixes the "python setup.py develop" case (also 'install' and
- # 'easy_install .'), in which subdependencies of the main project are
- # built (using setup.py bdist_egg) in the same python process. Assume
- # a main project A and a dependency B, which use different versions
- # of Versioneer. A's setup.py imports A's Versioneer, leaving it in
- # sys.modules by the time B's setup.py is executed, causing B to run
- # with the wrong versioneer. Setuptools wraps the sub-dep builds in a
- # sandbox that restores sys.modules to it's pre-build state, so the
- # parent is protected against the child's "import versioneer". By
- # removing ourselves from sys.modules here, before the child build
- # happens, we protect the child from the parent's versioneer too.
- # Also see https://github.com/warner/python-versioneer/issues/52
-
- cmds = {}
-
- # we add "version" to both distutils and setuptools
- from distutils.core import Command
-
- class cmd_version(Command):
- description = "report generated version string"
- user_options = []
- boolean_options = []
-
- def initialize_options(self):
- pass
-
- def finalize_options(self):
- pass
-
- def run(self):
- vers = get_versions(verbose=True)
- print("Version: %s" % vers["version"])
- print(" full-revisionid: %s" % vers.get("full-revisionid"))
- print(" dirty: %s" % vers.get("dirty"))
- print(" date: %s" % vers.get("date"))
- if vers["error"]:
- print(" error: %s" % vers["error"])
- cmds["version"] = cmd_version
-
- # we override "build_py" in both distutils and setuptools
- #
- # most invocation pathways end up running build_py:
- # distutils/build -> build_py
- # distutils/install -> distutils/build ->..
- # setuptools/bdist_wheel -> distutils/install ->..
- # setuptools/bdist_egg -> distutils/install_lib -> build_py
- # setuptools/install -> bdist_egg ->..
- # setuptools/develop -> ?
- # pip install:
- # copies source tree to a tempdir before running egg_info/etc
- # if .git isn't copied too, 'git describe' will fail
- # then does setup.py bdist_wheel, or sometimes setup.py install
- # setup.py egg_info -> ?
-
- # we override different "build_py" commands for both environments
- if "setuptools" in sys.modules:
- from setuptools.command.build_py import build_py as _build_py
- else:
- from distutils.command.build_py import build_py as _build_py
-
- class cmd_build_py(_build_py):
- def run(self):
- root = get_root()
- cfg = get_config_from_root(root)
- versions = get_versions()
- _build_py.run(self)
- # now locate _version.py in the new build/ directory and replace
- # it with an updated value
- if cfg.versionfile_build:
- target_versionfile = os.path.join(self.build_lib,
- cfg.versionfile_build)
- print("UPDATING %s" % target_versionfile)
- write_to_version_file(target_versionfile, versions)
- cmds["build_py"] = cmd_build_py
-
- if "cx_Freeze" in sys.modules: # cx_freeze enabled?
- from cx_Freeze.dist import build_exe as _build_exe
- # nczeczulin reports that py2exe won't like the pep440-style string
- # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g.
- # setup(console=[{
- # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION
- # "product_version": versioneer.get_version(),
- # ...
-
- class cmd_build_exe(_build_exe):
- def run(self):
- root = get_root()
- cfg = get_config_from_root(root)
- versions = get_versions()
- target_versionfile = cfg.versionfile_source
- print("UPDATING %s" % target_versionfile)
- write_to_version_file(target_versionfile, versions)
-
- _build_exe.run(self)
- os.unlink(target_versionfile)
- with open(cfg.versionfile_source, "w") as f:
- LONG = LONG_VERSION_PY[cfg.VCS]
- f.write(LONG %
- {"DOLLAR": "$",
- "STYLE": cfg.style,
- "TAG_PREFIX": cfg.tag_prefix,
- "PARENTDIR_PREFIX": cfg.parentdir_prefix,
- "VERSIONFILE_SOURCE": cfg.versionfile_source,
- })
- cmds["build_exe"] = cmd_build_exe
- del cmds["build_py"]
-
- if 'py2exe' in sys.modules: # py2exe enabled?
- try:
- from py2exe.distutils_buildexe import py2exe as _py2exe # py3
- except ImportError:
- from py2exe.build_exe import py2exe as _py2exe # py2
-
- class cmd_py2exe(_py2exe):
- def run(self):
- root = get_root()
- cfg = get_config_from_root(root)
- versions = get_versions()
- target_versionfile = cfg.versionfile_source
- print("UPDATING %s" % target_versionfile)
- write_to_version_file(target_versionfile, versions)
-
- _py2exe.run(self)
- os.unlink(target_versionfile)
- with open(cfg.versionfile_source, "w") as f:
- LONG = LONG_VERSION_PY[cfg.VCS]
- f.write(LONG %
- {"DOLLAR": "$",
- "STYLE": cfg.style,
- "TAG_PREFIX": cfg.tag_prefix,
- "PARENTDIR_PREFIX": cfg.parentdir_prefix,
- "VERSIONFILE_SOURCE": cfg.versionfile_source,
- })
- cmds["py2exe"] = cmd_py2exe
-
- # we override different "sdist" commands for both environments
- if "setuptools" in sys.modules:
- from setuptools.command.sdist import sdist as _sdist
- else:
- from distutils.command.sdist import sdist as _sdist
-
- class cmd_sdist(_sdist):
- def run(self):
- versions = get_versions()
- self._versioneer_generated_versions = versions
- # unless we update this, the command will keep using the old
- # version
- self.distribution.metadata.version = versions["version"]
- return _sdist.run(self)
-
- def make_release_tree(self, base_dir, files):
- root = get_root()
- cfg = get_config_from_root(root)
- _sdist.make_release_tree(self, base_dir, files)
- # now locate _version.py in the new base_dir directory
- # (remembering that it may be a hardlink) and replace it with an
- # updated value
- target_versionfile = os.path.join(base_dir, cfg.versionfile_source)
- print("UPDATING %s" % target_versionfile)
- write_to_version_file(target_versionfile,
- self._versioneer_generated_versions)
- cmds["sdist"] = cmd_sdist
-
- return cmds
-
-
-CONFIG_ERROR = """
-setup.cfg is missing the necessary Versioneer configuration. You need
-a section like:
-
- [versioneer]
- VCS = git
- style = pep440
- versionfile_source = src/myproject/_version.py
- versionfile_build = myproject/_version.py
- tag_prefix =
- parentdir_prefix = myproject-
-
-You will also need to edit your setup.py to use the results:
-
- import versioneer
- setup(version=versioneer.get_version(),
- cmdclass=versioneer.get_cmdclass(), ...)
-
-Please read the docstring in ./versioneer.py for configuration instructions,
-edit setup.cfg, and re-run the installer or 'python versioneer.py setup'.
-"""
-
-SAMPLE_CONFIG = """
-# See the docstring in versioneer.py for instructions. Note that you must
-# re-run 'versioneer.py setup' after changing this section, and commit the
-# resulting files.
-
-[versioneer]
-#VCS = git
-#style = pep440
-#versionfile_source =
-#versionfile_build =
-#tag_prefix =
-#parentdir_prefix =
-
-"""
-
-INIT_PY_SNIPPET = """
-from ._version import get_versions
-__version__ = get_versions()['version']
-del get_versions
-"""
-
-
-def do_setup():
- """Main VCS-independent setup function for installing Versioneer."""
- root = get_root()
- try:
- cfg = get_config_from_root(root)
- except (EnvironmentError, configparser.NoSectionError,
- configparser.NoOptionError) as e:
- if isinstance(e, (EnvironmentError, configparser.NoSectionError)):
- print("Adding sample versioneer config to setup.cfg",
- file=sys.stderr)
- with open(os.path.join(root, "setup.cfg"), "a") as f:
- f.write(SAMPLE_CONFIG)
- print(CONFIG_ERROR, file=sys.stderr)
- return 1
-
- print(" creating %s" % cfg.versionfile_source)
- with open(cfg.versionfile_source, "w") as f:
- LONG = LONG_VERSION_PY[cfg.VCS]
- f.write(LONG % {"DOLLAR": "$",
- "STYLE": cfg.style,
- "TAG_PREFIX": cfg.tag_prefix,
- "PARENTDIR_PREFIX": cfg.parentdir_prefix,
- "VERSIONFILE_SOURCE": cfg.versionfile_source,
- })
-
- ipy = os.path.join(os.path.dirname(cfg.versionfile_source),
- "__init__.py")
- if os.path.exists(ipy):
- try:
- with open(ipy, "r") as f:
- old = f.read()
- except EnvironmentError:
- old = ""
- if INIT_PY_SNIPPET not in old:
- print(" appending to %s" % ipy)
- with open(ipy, "a") as f:
- f.write(INIT_PY_SNIPPET)
- else:
- print(" %s unmodified" % ipy)
- else:
- print(" %s doesn't exist, ok" % ipy)
- ipy = None
-
- # Make sure both the top-level "versioneer.py" and versionfile_source
- # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so
- # they'll be copied into source distributions. Pip won't be able to
- # install the package without this.
- manifest_in = os.path.join(root, "MANIFEST.in")
- simple_includes = set()
- try:
- with open(manifest_in, "r") as f:
- for line in f:
- if line.startswith("include "):
- for include in line.split()[1:]:
- simple_includes.add(include)
- except EnvironmentError:
- pass
- # That doesn't cover everything MANIFEST.in can do
- # (http://docs.python.org/2/distutils/sourcedist.html#commands), so
- # it might give some false negatives. Appending redundant 'include'
- # lines is safe, though.
- if "versioneer.py" not in simple_includes:
- print(" appending 'versioneer.py' to MANIFEST.in")
- with open(manifest_in, "a") as f:
- f.write("include versioneer.py\n")
- else:
- print(" 'versioneer.py' already in MANIFEST.in")
- if cfg.versionfile_source not in simple_includes:
- print(" appending versionfile_source ('%s') to MANIFEST.in" %
- cfg.versionfile_source)
- with open(manifest_in, "a") as f:
- f.write("include %s\n" % cfg.versionfile_source)
- else:
- print(" versionfile_source already in MANIFEST.in")
-
- # Make VCS-specific changes. For git, this means creating/changing
- # .gitattributes to mark _version.py for export-subst keyword
- # substitution.
- do_vcs_install(manifest_in, cfg.versionfile_source, ipy)
- return 0
-
-
-def scan_setup_py():
- """Validate the contents of setup.py against Versioneer's expectations."""
- found = set()
- setters = False
- errors = 0
- with open("setup.py", "r") as f:
- for line in f.readlines():
- if "import versioneer" in line:
- found.add("import")
- if "versioneer.get_cmdclass()" in line:
- found.add("cmdclass")
- if "versioneer.get_version()" in line:
- found.add("get_version")
- if "versioneer.VCS" in line:
- setters = True
- if "versioneer.versionfile_source" in line:
- setters = True
- if len(found) != 3:
- print("")
- print("Your setup.py appears to be missing some important items")
- print("(but I might be wrong). Please make sure it has something")
- print("roughly like the following:")
- print("")
- print(" import versioneer")
- print(" setup( version=versioneer.get_version(),")
- print(" cmdclass=versioneer.get_cmdclass(), ...)")
- print("")
- errors += 1
- if setters:
- print("You should remove lines like 'versioneer.VCS = ' and")
- print("'versioneer.versionfile_source = ' . This configuration")
- print("now lives in setup.cfg, and should be removed from setup.py")
- print("")
- errors += 1
- return errors
-
-
-if __name__ == "__main__":
- cmd = sys.argv[1]
- if cmd == "setup":
- errors = do_setup()
- errors += scan_setup_py()
- if errors:
- sys.exit(1)
View it on GitLab: https://salsa.debian.org/med-team/python-questplus/-/commit/d015787fb84d239ebb100a9aecadee79567b2a21
--
This project does not include diff previews in email notifications.
View it on GitLab: https://salsa.debian.org/med-team/python-questplus/-/commit/d015787fb84d239ebb100a9aecadee79567b2a21
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20240716/fb2d719e/attachment-0001.htm>
More information about the debian-med-commit
mailing list