[med-svn] [Git][med-team/python-epimodels][master] 5 commits: routine-update: Fix watchfile to detect new versions on github
Steffen Möller (@moeller)
gitlab at salsa.debian.org
Fri Sep 3 15:16:51 BST 2021
Steffen Möller pushed to branch master at Debian Med / python-epimodels
Commits:
4fcb8e5b by Steffen Moeller at 2021-09-03T16:06:46+02:00
routine-update: Fix watchfile to detect new versions on github
- - - - -
f4d63746 by Steffen Moeller at 2021-09-03T16:06:49+02:00
routine-update: New upstream version
- - - - -
be5db31b by Steffen Moeller at 2021-09-03T16:06:50+02:00
New upstream version 0.3.20
- - - - -
90bc6326 by Steffen Moeller at 2021-09-03T16:06:51+02:00
Update upstream source from tag 'upstream/0.3.20'
Update to upstream version '0.3.20'
with Debian dir 7fb92572900fe2cb77424212b77819cba4b157cd
- - - - -
8d5e96ce by Steffen Moeller at 2021-09-03T16:16:28+02:00
Initial series of updates.
- - - - -
16 changed files:
- + .github/workflows/python-package.yml
- − Pipfile
- − Pipfile.lock
- + condarecipe/epimodels/meta.yaml
- debian/changelog
- debian/control
- debian/patches/ignore_pyscaffold.patch
- debian/upstream/metadata
- debian/watch
- docs/Makefile
- docs/conf.py
- requirements.txt
- setup.cfg
- setup.py
- src/epimodels/__init__.py
- src/epimodels/tools/phase.py
Changes:
=====================================
.github/workflows/python-package.yml
=====================================
@@ -0,0 +1,39 @@
+# 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: Python package
+
+on:
+ push:
+ branches: [ master ]
+ pull_request:
+ branches: [ master ]
+
+jobs:
+ build:
+
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: [3.6, 3.7, 3.8]
+
+ steps:
+ - uses: actions/checkout at v2
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python at v2
+ with:
+ python-version: ${{ matrix.python-version }}
+ - name: Install dependencies
+ run: |
+ python -m pip install --upgrade pip
+ pip install flake8 pytest
+ if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+ - name: Lint with flake8
+ run: |
+ # stop the build if there are Python syntax errors or undefined names
+ flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+ # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+ flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+ - name: Test with pytest
+ run: |
+ pytest
=====================================
Pipfile deleted
=====================================
@@ -1,22 +0,0 @@
-[[source]]
-url = "https://pypi.org/simple"
-verify_ssl = true
-name = "pypi"
-
-[packages]
-cython = "*"
-numpy = "*"
-scipy = "*"
-sympy = "*"
-pytest = "*"
-pytest-cov = "*"
-matplotlib = "*"
-mypy = "*"
-sphinx = "*"
-pyitlib = "*"
-numba = "*"
-
-[dev-packages]
-
-[requires]
-python_version = "3.7"
=====================================
Pipfile.lock deleted
=====================================
@@ -1,593 +0,0 @@
-{
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- "pipfile-spec": 6,
- "requires": {
- "python_version": "3.7"
- },
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- "url": "https://pypi.org/simple",
- "verify_ssl": true
- }
- ]
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- "sha256:630968c5cdee51a11c05a30453f8cd65e0cc1d2ad0d9192819df9978984529f4",
- "sha256:66480f95b8167c9c5c5c87f32cf437d585937970f3fc24386f313a4c97b44e34",
- "sha256:71211d26ffd12d63a83e079ff258ac9d56a1376a25bc80b1cdcdf601b855b90b",
- "sha256:95bd11af7eafc16e829af2d3df510cecfd4387f6453355188342c3e79a2ec87a",
- "sha256:bc6c7d3fa1325a0c6613512a093bc2a2a15aeec350451cbdf9e1d4bffe3e3233",
- "sha256:cc34a6f5b426748a507dd5d1de4c1978f2eb5626d51326e43280941206c209e1",
- "sha256:d755f03c1e4a51e9b24d899561fec4ccaf51f210d52abdf8c07ee2849b212a36",
- "sha256:d7c45933b1bdfaf9f36c579671fec15d25b06c8398f113dab64c18ed1adda01d",
- "sha256:d896919306dd0aa22d0132f62a1b78d11aaf4c9fc5b3410d3c666b818191630a",
- "sha256:ffde2fbfad571af120fcbfbbc61c72469e72f550d676c3342492a9dfdefb8f12"
- ],
- "version": "==1.4.0"
- },
- "typing-extensions": {
- "hashes": [
- "sha256:2ed632b30bb54fc3941c382decfd0ee4148f5c591651c9272473fea2c6397d95",
- "sha256:b1edbbf0652660e32ae780ac9433f4231e7339c7f9a8057d0f042fcbcea49b87",
- "sha256:d8179012ec2c620d3791ca6fe2bf7979d979acdbef1fca0bc56b37411db682ed"
- ],
- "version": "==3.7.4"
- },
- "urllib3": {
- "hashes": [
- "sha256:b246607a25ac80bedac05c6f282e3cdaf3afb65420fd024ac94435cabe6e18d1",
- "sha256:dbe59173209418ae49d485b87d1681aefa36252ee85884c31346debd19463232"
- ],
- "version": "==1.25.3"
- },
- "wcwidth": {
- "hashes": [
- "sha256:3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e",
- "sha256:f4ebe71925af7b40a864553f761ed559b43544f8f71746c2d756c7fe788ade7c"
- ],
- "version": "==0.1.7"
- },
- "zipp": {
- "hashes": [
- "sha256:3718b1cbcd963c7d4c5511a8240812904164b7f381b647143a89d3b98f9bcd8e",
- "sha256:f06903e9f1f43b12d371004b4ac7b06ab39a44adc747266928ae6debfa7b3335"
- ],
- "version": "==0.6.0"
- }
- },
- "develop": {}
-}
=====================================
condarecipe/epimodels/meta.yaml
=====================================
@@ -0,0 +1,34 @@
+{% set name = "epimodels" %}
+{% set version = "0.3.19" %}
+
+package:
+ name: "{{ name|lower }}"
+ version: "{{ version }}"
+
+source:
+ url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
+ sha256: 8dec0de96e6ec506e3c61b7af6d687791c6db0eb5f74a90538f2844505db60e8
+
+build:
+ number: 0
+ script: "{{ PYTHON }} -m pip install . -vv"
+
+requirements:
+ host:
+ - pip
+ - python
+ run:
+ - python
+
+about:
+ home: The package home page
+ license: mit
+ license_family: MIT
+ license_file:
+ summary: "Library of mathematical epidemic models for use in simulation studies and inference"
+ doc_url:
+ dev_url:
+
+extra:
+ recipe-maintainers:
+ - your-github-id-here
=====================================
debian/changelog
=====================================
@@ -1,3 +1,21 @@
+python-epimodels (0.3.20-1) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * New upstream version
+ * d/u/metadata: Added ref to conda
+ * Standards-Version: 4.6.0 (routine-update)
+
+ TODO: Tests fail because of failing X connection?!?
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 03 Sep 2021 16:06:49 +0200
+
+python-epimodels (0.3.18-3.1) UNRELEASED; urgency=medium
+
+ * Non-maintainer upload.
+ * Fix watchfile to detect new versions on github (routine-update)
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 03 Sep 2021 16:06:46 +0200
+
python-epimodels (0.3.18-3) unstable; urgency=medium
* Team Upload.
=====================================
debian/control
=====================================
@@ -12,7 +12,7 @@ Build-Depends: debhelper-compat (= 13),
python3-scipy <!nocheck>,
python3-pytest <!nocheck>,
python3-pytest-cov <!nocheck>
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/python-epimodels
Vcs-Git: https://salsa.debian.org/med-team/python-epimodels.git
Homepage: https://github.com/fccoelho/epimodels
=====================================
debian/patches/ignore_pyscaffold.patch
=====================================
@@ -2,32 +2,16 @@ Author: Andreas Tille <tille at debian.org>
Last-Update: Sun, 21 Feb 2021 18:38:03 +0100
Description: Avoid usage of pyscaffold
---- a/setup.py
-+++ b/setup.py
-@@ -20,4 +20,4 @@ except VersionConflict:
-
-
- if __name__ == "__main__":
-- setup(use_pyscaffold=True)
-+ setup(use_pyscaffold=False)
---- a/setup.cfg
-+++ b/setup.cfg
-@@ -25,7 +25,7 @@ include_package_data = True
- package_dir =
- =src
- # DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
--setup_requires = pyscaffold>=3.2a0,<3.3a0
-+# setup_requires = pyscaffold>=3.2a0,<3.3a0
- # Add here dependencies of your project (semicolon/line-separated), e.g..
- install_requires = numpy; scipy; cython
- # The usage of test_requires is discouraged, see `Dependency Management` docs
-@@ -77,24 +77,10 @@ norecursedirs =
+Index: python-epimodels/setup.cfg
+===================================================================
+--- python-epimodels.orig/setup.cfg
++++ python-epimodels/setup.cfg
+@@ -80,25 +80,10 @@ norecursedirs =
.tox
testpaths = tests
-[aliases]
--build = bdist_wheel
--release = build upload
+-release = sdist bdist_wheel upload
-
-[bdist_wheel]
-# Use this option if your package is pure-python
@@ -41,17 +25,20 @@ Description: Avoid usage of pyscaffold
-# Options for the devpi: PyPI server and packaging tool
-# VCS export must be deactivated since we are using setuptools-scm
-no-vcs = 1
--formats = bdist_wheel
+-formats =
+- sdist
+- bdist_wheel
-
[flake8]
# Some sane defaults for the code style checker flake8
exclude =
-@@ -104,8 +90,3 @@ exclude =
+@@ -107,9 +92,3 @@ exclude =
+ dist
.eggs
docs/conf.py
-
+-
-[pyscaffold]
-# PyScaffold's parameters when the project was created.
-# This will be used when updating. Do not change!
--version = 3.2.3
+-version = 4.0
-package = epimodels
=====================================
debian/upstream/metadata
=====================================
@@ -3,3 +3,9 @@ Bug-Database: https://github.com/fccoelho/epimodels/issues
Bug-Submit: https://github.com/fccoelho/epimodels/issues/new
Repository: https://github.com/fccoelho/epimodels.git
Repository-Browse: https://github.com/fccoelho/epimodels
+Registry:
+ - Name: conda:fccoelho
+ Entry: epimodels
+ - Name: bio.tools
+ Entry: NA
+ Checked: 2021-09-03
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/fccoelho/epimodels/releases .*/archive/v?@ANY_VERSION@\.tar\.gz
+ https://github.com/fccoelho/epimodels/releases .*/v?@ANY_VERSION@\.tar\.gz
=====================================
docs/Makefile
=====================================
@@ -1,193 +1,29 @@
# Makefile for Sphinx documentation
#
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-PAPER =
-BUILDDIR = ../build/sphinx/
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
AUTODOCDIR = api
-AUTODOCBUILD = sphinx-apidoc
-PROJECT = epimodels
-MODULEDIR = ../src/epimodels
# User-friendly check for sphinx-build
ifeq ($(shell which $(SPHINXBUILD) >/dev/null 2>&1; echo $?), 1)
-$(error The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/)
+$(error "The '$(SPHINXBUILD)' command was not found. Make sure you have Sphinx installed, then set the SPHINXBUILD environment variable to point to the full path of the '$(SPHINXBUILD)' executable. Alternatively you can add the directory with the executable to your PATH. If you don't have Sphinx installed, grab it from http://sphinx-doc.org/")
endif
-# Internal variables.
-PAPEROPT_a4 = -D latex_paper_size=a4
-PAPEROPT_letter = -D latex_paper_size=letter
-ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-# the i18n builder cannot share the environment and doctrees with the others
-I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) .
-
-.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext doc-requirements
+.PHONY: help clean Makefile
+# Put it first so that "make" without argument is like "make help".
help:
- @echo "Please use \`make <target>' where <target> is one of"
- @echo " html to make standalone HTML files"
- @echo " dirhtml to make HTML files named index.html in directories"
- @echo " singlehtml to make a single large HTML file"
- @echo " pickle to make pickle files"
- @echo " json to make JSON files"
- @echo " htmlhelp to make HTML files and a HTML help project"
- @echo " qthelp to make HTML files and a qthelp project"
- @echo " devhelp to make HTML files and a Devhelp project"
- @echo " epub to make an epub"
- @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
- @echo " latexpdf to make LaTeX files and run them through pdflatex"
- @echo " latexpdfja to make LaTeX files and run them through platex/dvipdfmx"
- @echo " text to make text files"
- @echo " man to make manual pages"
- @echo " texinfo to make Texinfo files"
- @echo " info to make Texinfo files and run them through makeinfo"
- @echo " gettext to make PO message catalogs"
- @echo " changes to make an overview of all changed/added/deprecated items"
- @echo " xml to make Docutils-native XML files"
- @echo " pseudoxml to make pseudoxml-XML files for display purposes"
- @echo " linkcheck to check all external links for integrity"
- @echo " doctest to run all doctests embedded in the documentation (if enabled)"
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
clean:
rm -rf $(BUILDDIR)/* $(AUTODOCDIR)
-$(AUTODOCDIR): $(MODULEDIR)
- mkdir -p $@
- $(AUTODOCBUILD) -f -o $@ $^
-
-doc-requirements: $(AUTODOCDIR)
-
-html: doc-requirements
- $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
-
-dirhtml: doc-requirements
- $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
- @echo
- @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
-
-singlehtml: doc-requirements
- $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml
- @echo
- @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml."
-
-pickle: doc-requirements
- $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
- @echo
- @echo "Build finished; now you can process the pickle files."
-
-json: doc-requirements
- $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
- @echo
- @echo "Build finished; now you can process the JSON files."
-
-htmlhelp: doc-requirements
- $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp
- @echo
- @echo "Build finished; now you can run HTML Help Workshop with the" \
- ".hhp project file in $(BUILDDIR)/htmlhelp."
-
-qthelp: doc-requirements
- $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp
- @echo
- @echo "Build finished; now you can run "qcollectiongenerator" with the" \
- ".qhcp project file in $(BUILDDIR)/qthelp, like this:"
- @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/$(PROJECT).qhcp"
- @echo "To view the help file:"
- @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/$(PROJECT).qhc"
-
-devhelp: doc-requirements
- $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp
- @echo
- @echo "Build finished."
- @echo "To view the help file:"
- @echo "# mkdir -p $HOME/.local/share/devhelp/$(PROJECT)"
- @echo "# ln -s $(BUILDDIR)/devhelp $HOME/.local/share/devhelp/$(PROJEC)"
- @echo "# devhelp"
-
-epub: doc-requirements
- $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub
- @echo
- @echo "Build finished. The epub file is in $(BUILDDIR)/epub."
-
-patch-latex:
- find _build/latex -iname "*.tex" | xargs -- \
- sed -i'' 's~includegraphics{~includegraphics\[keepaspectratio,max size={\\textwidth}{\\textheight}\]{~g'
-
-latex: doc-requirements
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- $(MAKE) patch-latex
- @echo
- @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
- @echo "Run \`make' in that directory to run these through (pdf)latex" \
- "(use \`make latexpdf' here to do that automatically)."
-
-latexpdf: doc-requirements
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- $(MAKE) patch-latex
- @echo "Running LaTeX files through pdflatex..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-latexpdfja: doc-requirements
- $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
- @echo "Running LaTeX files through platex and dvipdfmx..."
- $(MAKE) -C $(BUILDDIR)/latex all-pdf-ja
- @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
-
-text: doc-requirements
- $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text
- @echo
- @echo "Build finished. The text files are in $(BUILDDIR)/text."
-
-man: doc-requirements
- $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man
- @echo
- @echo "Build finished. The manual pages are in $(BUILDDIR)/man."
-
-texinfo: doc-requirements
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo
- @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo."
- @echo "Run \`make' in that directory to run these through makeinfo" \
- "(use \`make info' here to do that automatically)."
-
-info: doc-requirements
- $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo
- @echo "Running Texinfo files through makeinfo..."
- make -C $(BUILDDIR)/texinfo info
- @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo."
-
-gettext: doc-requirements
- $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale
- @echo
- @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale."
-
-changes: doc-requirements
- $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
- @echo
- @echo "The overview file is in $(BUILDDIR)/changes."
-
-linkcheck: doc-requirements
- $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
- @echo
- @echo "Link check complete; look for any errors in the above output " \
- "or in $(BUILDDIR)/linkcheck/output.txt."
-
-doctest: doc-requirements
- $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
- @echo "Testing of doctests in the sources finished, look at the " \
- "results in $(BUILDDIR)/doctest/output.txt."
-
-xml: doc-requirements
- $(SPHINXBUILD) -b xml $(ALLSPHINXOPTS) $(BUILDDIR)/xml
- @echo
- @echo "Build finished. The XML files are in $(BUILDDIR)/xml."
-
-pseudoxml: doc-requirements
- $(SPHINXBUILD) -b pseudoxml $(ALLSPHINXOPTS) $(BUILDDIR)/pseudoxml
- @echo
- @echo "Build finished. The pseudo-XML files are in $(BUILDDIR)/pseudoxml."
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
=====================================
docs/conf.py
=====================================
@@ -1,9 +1,8 @@
-# -*- coding: utf-8 -*-
-#
# This file is execfile()d with the current directory set to its containing dir.
#
-# Note that not all possible configuration values are present in this
-# autogenerated file.
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
#
# All configuration values have a default; values that are commented out
# serve to show the default.
@@ -13,15 +12,18 @@ import sys
import inspect
import shutil
-__location__ = os.path.join(os.getcwd(), os.path.dirname(
- inspect.getfile(inspect.currentframe())))
+# -- Path setup --------------------------------------------------------------
+
+__location__ = os.path.join(
+ os.getcwd(), os.path.dirname(inspect.getfile(inspect.currentframe()))
+)
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.insert(0, os.path.join(__location__, '../src'))
+sys.path.insert(0, os.path.join(__location__, "../src"))
-# -- Run sphinx-apidoc ------------------------------------------------------
+# -- Run sphinx-apidoc -------------------------------------------------------
# This hack is necessary since RTD does not issue `sphinx-apidoc` before running
# `sphinx-build -b html . _build/html`. See Issue:
# https://github.com/rtfd/readthedocs.org/issues/1139
@@ -43,55 +45,65 @@ except FileNotFoundError:
try:
import sphinx
- from pkg_resources import parse_version
- cmd_line_template = "sphinx-apidoc -f -o {outputdir} {moduledir}"
+ cmd_line_template = (
+ "sphinx-apidoc --implicit-namespaces -f -o {outputdir} {moduledir}"
+ )
cmd_line = cmd_line_template.format(outputdir=output_dir, moduledir=module_dir)
args = cmd_line.split(" ")
- if parse_version(sphinx.__version__) >= parse_version('1.7'):
+ if tuple(sphinx.__version__.split(".")) >= ("1", "7"):
+ # This is a rudimentary parse_version to avoid external dependencies
args = args[1:]
apidoc.main(args)
except Exception as e:
print("Running `sphinx-apidoc` failed!\n{}".format(e))
-# -- General configuration -----------------------------------------------------
+# -- General configuration ---------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
# needs_sphinx = '1.0'
# Add any Sphinx extension module names here, as strings. They can be extensions
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
- 'sphinx.ext.autosummary', 'sphinx.ext.viewcode', 'sphinx.ext.coverage',
- 'sphinx.ext.doctest', 'sphinx.ext.ifconfig', 'sphinx.ext.mathjax',
- 'sphinx.ext.napoleon']
+extensions = [
+ "sphinx.ext.autodoc",
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.todo",
+ "sphinx.ext.autosummary",
+ "sphinx.ext.viewcode",
+ "sphinx.ext.coverage",
+ "sphinx.ext.doctest",
+ "sphinx.ext.ifconfig",
+ "sphinx.ext.mathjax",
+ "sphinx.ext.napoleon",
+]
# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
# The suffix of source filenames.
-source_suffix = '.rst'
+source_suffix = ".rst"
# The encoding of source files.
# source_encoding = 'utf-8-sig'
# The master toctree document.
-master_doc = 'index'
+master_doc = "index"
# General information about the project.
-project = u'epimodels'
-copyright = u'2020, Flávio Codeço Coelho'
+project = "epimodels"
+copyright = "2021, Flávio Codeço Coelho"
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
-version = '' # Is set by calling `setup.py docs`
+version = "" # Is set by calling `setup.py docs`
# The full version, including alpha/beta/rc tags.
-release = '' # Is set by calling `setup.py docs`
+release = "" # Is set by calling `setup.py docs`
# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
@@ -105,7 +117,7 @@ release = '' # Is set by calling `setup.py docs`
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
-exclude_patterns = ['_build']
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", ".venv"]
# The reST default role (used for this markup: `text`) to use for all documents.
# default_role = None
@@ -122,7 +134,7 @@ exclude_patterns = ['_build']
# show_authors = False
# The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []
@@ -131,18 +143,18 @@ pygments_style = 'sphinx'
# keep_warnings = False
-# -- Options for HTML output ---------------------------------------------------
+# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
-html_theme = 'alabaster'
+html_theme = "alabaster"
# Theme options are theme-specific and customize the look and feel of a theme
# further. For a list of options available for each theme, see the
# documentation.
html_theme_options = {
- 'sidebar_width': '300px',
- 'page_width': '1200px'
+ "sidebar_width": "300px",
+ "page_width": "1200px"
}
# Add any paths that contain custom themes here, relative to this directory.
@@ -172,7 +184,7 @@ else:
# 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"]
# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
# using the given strftime format.
@@ -216,27 +228,24 @@ html_static_path = ['_static']
# html_file_suffix = None
# Output file base name for HTML help builder.
-htmlhelp_basename = 'epimodels-doc'
+htmlhelp_basename = "epimodels-doc"
-# -- Options for LaTeX output --------------------------------------------------
+# -- Options for LaTeX output ------------------------------------------------
latex_elements = {
-# The paper size ('letterpaper' or 'a4paper').
-# 'papersize': 'letterpaper',
-
-# The font size ('10pt', '11pt' or '12pt').
-# 'pointsize': '10pt',
-
-# Additional stuff for the LaTeX preamble.
-# 'preamble': '',
+ # The paper size ("letterpaper" or "a4paper").
+ # "papersize": "letterpaper",
+ # The font size ("10pt", "11pt" or "12pt").
+ # "pointsize": "10pt",
+ # Additional stuff for the LaTeX preamble.
+ # "preamble": "",
}
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('index', 'user_guide.tex', u'epimodels Documentation',
- u'Flávio Codeço Coelho', 'manual'),
+ ("index", "user_guide.tex", "epimodels Documentation", "Flávio Codeço Coelho", "manual")
]
# The name of an image file (relative to this directory) to place at the top of
@@ -259,14 +268,15 @@ latex_documents = [
# If false, no module index is generated.
# latex_domain_indices = True
-# -- External mapping ------------------------------------------------------------
-python_version = '.'.join(map(str, sys.version_info[0:2]))
+# -- External mapping --------------------------------------------------------
+python_version = ".".join(map(str, sys.version_info[0:2]))
intersphinx_mapping = {
- 'sphinx': ('http://www.sphinx-doc.org/en/stable', None),
- 'python': ('https://docs.python.org/' + python_version, None),
- 'matplotlib': ('https://matplotlib.org', None),
- 'numpy': ('https://docs.scipy.org/doc/numpy', None),
- 'sklearn': ('http://scikit-learn.org/stable', None),
- 'pandas': ('http://pandas.pydata.org/pandas-docs/stable', None),
- 'scipy': ('https://docs.scipy.org/doc/scipy/reference', None),
+ "sphinx": ("http://www.sphinx-doc.org/en/stable", None),
+ "python": ("https://docs.python.org/" + python_version, None),
+ "matplotlib": ("https://matplotlib.org", None),
+ "numpy": ("https://docs.scipy.org/doc/numpy", None),
+ "sklearn": ("https://scikit-learn.org/stable", None),
+ "pandas": ("https://pandas.pydata.org/pandas-docs/stable", None),
+ "scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
+ "pyscaffold": ("https://pyscaffold.org/en/stable", None),
}
=====================================
requirements.txt
=====================================
@@ -1,17 +1,17 @@
-# =============================================================================
-# DEPRECATION WARNING:
-#
-# The file `requirements.txt` does not influence the package dependencies and
-# will not be automatically created in the next version of PyScaffold (v4.x).
-#
-# Please have look at the docs for better alternatives
-# (`Dependency Management` section).
-# =============================================================================
-#
# Add your pinned requirements so that they can be easily installed with:
# pip install -r requirements.txt
# Remember to also add them in setup.cfg but unpinned.
# Example:
# numpy==1.13.3
# scipy==1.0
-
+cython
+numpy
+scipy
+sympy
+pytest
+pytest-cov
+matplotlib
+mypy
+sphinx
+pyitlib
+numba
=====================================
setup.cfg
=====================================
@@ -20,14 +20,17 @@ classifiers =
[options]
zip_safe = False
-packages = find:
+packages = find_namespace:
include_package_data = True
package_dir =
=src
# DON'T CHANGE THE FOLLOWING LINE! IT WILL BE UPDATED BY PYSCAFFOLD!
-setup_requires = pyscaffold>=3.2a0,<3.3a0
# Add here dependencies of your project (semicolon/line-separated), e.g.
-install_requires = numpy; scipy; cython
+install_requires =
+ importlib-metadata; python_version<"3.8"
+ numpy
+ scipy
+ cython
# The usage of test_requires is discouraged, see `Dependency Management` docs
# tests_require = pytest; pytest-cov
# Require a specific Python version, e.g. Python 2.7 or >= 3.4
@@ -68,9 +71,9 @@ extras = True
# Specify command line options as you would do when invoking py.test directly.
# e.g. --cov-report html (or xml) for html/xml output or --junitxml junit.xml
# in order to write a coverage file that can be read by Jenkins.
-addopts =
- --cov epimodels --cov-report term-missing
- --verbose
+#addopts =
+# --cov epimodels --cov-report term-missing
+# --verbose
norecursedirs =
dist
build
@@ -78,8 +81,7 @@ norecursedirs =
testpaths = tests
[aliases]
-build = bdist_wheel
-release = build upload
+release = sdist bdist_wheel upload
[bdist_wheel]
# Use this option if your package is pure-python
@@ -93,7 +95,9 @@ build_dir = docs/_build
# Options for the devpi: PyPI server and packaging tool
# VCS export must be deactivated since we are using setuptools-scm
no-vcs = 1
-formats = bdist_wheel
+formats =
+ sdist
+ bdist_wheel
[flake8]
# Some sane defaults for the code style checker flake8
@@ -107,5 +111,5 @@ exclude =
[pyscaffold]
# PyScaffold's parameters when the project was created.
# This will be used when updating. Do not change!
-version = 3.2.3
+version = 4.0
package = epimodels
=====================================
setup.py
=====================================
@@ -1,23 +1,21 @@
-# -*- coding: utf-8 -*-
"""
Setup file for epimodels.
Use setup.cfg to configure your project.
- This file was generated with PyScaffold 3.2.3.
+ This file was generated with PyScaffold 4.0.
PyScaffold helps you to put up the scaffold of your new Python project.
Learn more under: https://pyscaffold.org/
"""
-import sys
-
-from pkg_resources import VersionConflict, require
from setuptools import setup
-try:
- require('setuptools>=38.3')
-except VersionConflict:
- print("Error: version of setuptools is too old (<38.3)!")
- sys.exit(1)
-
-
if __name__ == "__main__":
- setup(use_pyscaffold=True)
+ try:
+ setup(use_scm_version={"version_scheme": "no-guess-dev"})
+ except: # noqa
+ print(
+ "\n\nAn error occurred while building the project, "
+ "please ensure you have the most updated version of setuptools, "
+ "setuptools_scm and wheel with:\n"
+ " pip install -U setuptools setuptools_scm wheel\n\n"
+ )
+ raise
=====================================
src/epimodels/__init__.py
=====================================
@@ -1,23 +1,27 @@
-# -*- coding: utf-8 -*-
-from pkg_resources import get_distribution, DistributionNotFound
+import sys
+
+if sys.version_info[:2] >= (3, 8):
+ # TODO: Import directly (no need for conditional) when `python_requires = >= 3.8`
+ from importlib.metadata import PackageNotFoundError, version # pragma: no cover
+else:
+ from importlib_metadata import PackageNotFoundError, version # pragma: no cover
try:
# Change here if project is renamed and does not equal the package name
dist_name = __name__
- __version__ = get_distribution(dist_name).version
-except DistributionNotFound:
- __version__ = 'unknown'
+ __version__ = version(dist_name)
+except PackageNotFoundError: # pragma: no cover
+ __version__ = "unknown"
finally:
- del get_distribution, DistributionNotFound
+ del version, PackageNotFoundError
-from matplotlib import pyplot as P
+from matplotlib import pyplot as P
class BaseModel:
"""
Base class for all models both discrete and continuous
"""
-
def __init__(self):
self.name = None
self.model_type = None
@@ -25,17 +29,14 @@ class BaseModel:
self.parameters = {}
self.traces = {}
- def plot_traces(self, vars: list = []):
+ def plot_traces(self, vars: list=[]):
"""
Plots the simulations
:param vars: variables to plot
"""
- if vars == []: # Plot all
- vars = [s for s in self.traces if s != 'time']
-
for series, data in self.traces.items():
- if series in vars:
+ if series in self.state_variables:
P.plot(self.traces['time'], data, label=series)
P.legend(loc=0)
P.grid()
- P.title("{} model".format(self.model_type))
+ P.title("{} model".format(self.model_type))
\ No newline at end of file
=====================================
src/epimodels/tools/phase.py
=====================================
@@ -12,31 +12,31 @@ Created on 29/11/18
by fccoelho
license: GPL V3 or Later
"""
-import numpy
-from pyitlib import discrete_random_variable as drv
-import pylab as P
-
-class TimeDelayEmbedding:
- def __init__(self, traces):
- self.traces = traces
-
- def mutual_information(self, data, tau_max=100):
- mis = []
-
- for tau in range(1, tau_max):
- unlagged = data[:-tau]
- lagged = numpy.roll(data, -tau)[:-tau]
- joint = numpy.hstack((unlagged, lagged))
- mis.append(drv.information_multi(joint))
- if len(mis) > 1 and mis[-2] < mis[-1]: # return first local minima
- tau -= 1
- return tau, mis
-
- def _find_embedding_dimension(self, x, tau):
- d = 2
- while true:
- ai = max([])
-
- def show_mutual_information(self, mis):
- P.plot(mis)
- P.show()
+# import numpy
+# # from pyitlib import discrete_random_variable as drv
+# import pylab as P
+#
+# class TimeDelayEmbedding:
+# def __init__(self, traces):
+# self.traces = traces
+#
+# def mutual_information(self, data, tau_max=100):
+# mis = []
+#
+# for tau in range(1, tau_max):
+# unlagged = data[:-tau]
+# lagged = numpy.roll(data, -tau)[:-tau]
+# joint = numpy.hstack((unlagged, lagged))
+# mis.append(drv.information_multi(joint))
+# if len(mis) > 1 and mis[-2] < mis[-1]: # return first local minima
+# tau -= 1
+# return tau, mis
+#
+# def _find_embedding_dimension(self, x, tau):
+# d = 2
+# while True:
+# ai = max([])
+#
+# def show_mutual_information(self, mis):
+# P.plot(mis)
+# P.show()
View it on GitLab: https://salsa.debian.org/med-team/python-epimodels/-/compare/376151a117cb1bbc9d184c615423f4da6384624b...8d5e96ce668393752d205a766306ccd46aad32ee
--
View it on GitLab: https://salsa.debian.org/med-team/python-epimodels/-/compare/376151a117cb1bbc9d184c615423f4da6384624b...8d5e96ce668393752d205a766306ccd46aad32ee
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