[med-svn] [Git][med-team/conda-package-handling][upstream] New upstream version 1.7.3
Nilesh Patra
gitlab at salsa.debian.org
Tue Apr 20 12:43:27 BST 2021
Nilesh Patra pushed to branch upstream at Debian Med / conda-package-handling
Commits:
7ca4d69c by Nilesh Patra at 2021-04-20T17:06:22+05:30
New upstream version 1.7.3
- - - - -
15 changed files:
- .authors.yml
- + .github/workflows/CI.yaml
- .mailmap
- .travis.yml
- AUTHORS.txt
- CHANGELOG.md
- appveyor.yml
- conda.recipe/meta.yaml
- + devtools/conda-envs/test_env.yaml
- src/conda_package_handling/_version.py
- src/conda_package_handling/api.py
- src/conda_package_handling/archive_utils_c.c
- src/conda_package_handling/cli.py
- src/conda_package_handling/tarball.py
- tests/test_api.py
Changes:
=====================================
.authors.yml
=====================================
@@ -25,10 +25,26 @@
github: alanhdu
- name: Ray Donnelly
email: mingw.android at gmail.com
- num_commits: 7
+ num_commits: 14
first_commit: 2020-05-06 10:49:55
+ github: mingwandroid
- name: ossdev07
email: ossdev at puresoftware.com
num_commits: 1
first_commit: 2020-01-06 10:18:31
github: ossdev07
+- name: leej3
+ email: johnleenimh at gmail.com
+ num_commits: 12
+ first_commit: 2021-02-23 12:20:16
+ github: leej3
+- name: Matthew R. Becker
+ email: beckermr at users.noreply.github.com
+ num_commits: 2
+ first_commit: 2020-12-29 14:58:11
+ github: beckermr
+- name: Eli Uriegas
+ email: seemethere101 at gmail.com
+ num_commits: 1
+ first_commit: 2021-03-14 08:41:18
+ github: seemethere
=====================================
.github/workflows/CI.yaml
=====================================
@@ -0,0 +1,63 @@
+name: CI
+
+on:
+ # GitHub has started calling new repo's first branch "main" https://github.com/github/renaming
+ # Existing codes likely still have "master" as the primary branch
+ # Both are tracked here to keep legacy and new codes working
+ push:
+ branches:
+ - "master"
+ - "main"
+ pull_request:
+ branches:
+ - "master"
+ - "main"
+
+jobs:
+ test:
+ name: Test on ${{ matrix.os }}, Python ${{ matrix.python-version }}
+ runs-on: ${{ matrix.os }}
+ strategy:
+ matrix:
+ os: [ubuntu-latest, windows-latest]
+ python-version: [3.7, 3.8, 3.9]
+
+ steps:
+ - uses: actions/checkout at v1
+
+ - name: Additional info about the build
+ shell: bash
+ run: |
+ uname -a
+ df -h
+ ulimit -a
+
+
+ # More info on options: https://github.com/conda-incubator/setup-miniconda
+ - uses: conda-incubator/setup-miniconda at v2
+ with:
+ python-version: ${{ matrix.python-version }}
+ environment-file: devtools/conda-envs/test_env.yaml
+
+ channels: defaults
+
+ activate-environment: test_env
+ auto-update-conda: false
+ auto-activate-base: false
+ show-channel-urls: true
+
+ - name: Install package
+
+ # conda setup requires this special shell
+ shell: bash -l {0}
+ run: |
+ conda build conda.recipe
+
+# TODO: Re-enable codecov when we figure out how to grab coverage from the conda build
+# environment
+# - name: CodeCov
+# uses: codecov/codecov-action at v1
+# with:
+# file: ./coverage.xml
+# flags: unittests
+# name: codecov-${{ matrix.os }}-py${{ matrix.python-version }}
=====================================
.mailmap
=====================================
@@ -11,8 +11,11 @@
Michael Sarahan <msarahan at gmail.com> Mike Sarahan <msarahan at continuum.io>
Michael Sarahan <msarahan at gmail.com> Mike Sarahan <msarahan at anaconda.com>
-Jonathan J. Helmus <jjhelmus at gmail.com>
Ray Donnelly <mingw.android at gmail.com>
+leej3 <johnleenimh at gmail.com>
+Jonathan J. Helmus <jjhelmus at gmail.com>
Nehal J Wani <nehaljw.kkd1 at gmail.com>
Alan Du <alanhdu at gmail.com>
+Matthew R. Becker <beckermr at users.noreply.github.com>
ossdev07 <ossdev at puresoftware.com>
+Eli Uriegas <seemethere101 at gmail.com>
=====================================
.travis.yml
=====================================
@@ -12,35 +12,42 @@ matrix:
env:
global:
- SUDO=""
+ - CONDA_ALWAYS_YES=1
install:
+ - set -e
- if [[ "${TRAVIS_CPU_ARCH}" == "arm64" ]]; then
- SUDO=sudo;
+ set -x;
+ # Archiconda install requires sudo for running commands. Pass the path
+ # through to the sudo environment so that condda is accessible
+ SUDO='sudo env PATH=$PATH'
wget -q "https://github.com/Archiconda/build-tools/releases/download/0.2.3/Archiconda3-0.2.3-Linux-aarch64.sh" -O archiconda.sh;
chmod +x archiconda.sh;
- export CONDA_ALWAYS_YES=1;
bash archiconda.sh -b -p $HOME/miniconda;
export PATH="$HOME/miniconda/bin:$PATH";
- $SUDO cp -r $HOME/miniconda/bin/* /usr/bin/;
- $SUDO conda install python=3.7 conda conda-build pytest six pytest-cov pytest-mock;
+ $SUDO conda install python=3.7 conda conda-build;
+ set +x;
else
- SUDO="";
wget https://repo.anaconda.com/pkgs/misc/conda-execs/conda-4.7.5-linux-64.exe -O conda.exe;
chmod +x conda.exe;
- export CONDA_ALWAYS_YES=1;
- ./conda.exe create -p $HOME/miniconda python=$TRAVIS_PYTHON_VERSION conda conda-build pytest six pytest-cov pytest-mock;
- fi
+ ./conda.exe create -p $HOME/miniconda python=$TRAVIS_PYTHON_VERSION conda conda-build;
+ fi;
- export PATH="$HOME/miniconda/bin:$PATH"
- hash -r
- if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
- conda install futures;
- fi
+ pip install futures mock pytest-cov pytest-mock;
+ else
+ pip3 install mock pytest-cov pytest-mock;
+ fi;
- $SUDO conda build conda.recipe --no-test
- $SUDO conda install --use-local conda-package-handling
- $SUDO conda info -a
script:
# rebuilding the recipe with our new CPH installed tests it a bit deeper than the test suite.
+ - which conda
- $SUDO conda build conda.recipe
- - pytest -v --color=yes --cov=conda_package_handling tests
+ # the system pytest is used for coverage testing, cph from current conda envorinment is used.
+ - which pytest
+ - pytest -v --color=yes -rA --cov=conda_package_handling tests
after_success:
- - conda install codecov
+ - $SUDO conda install codecov
- codecov
=====================================
AUTHORS.txt
=====================================
@@ -2,8 +2,11 @@ All of the people who have made at least one contribution to conda-package-handl
Authors are sorted by number of commits.
* Michael Sarahan
-* Jonathan J. Helmus
* Ray Donnelly
+* leej3
+* Jonathan J. Helmus
* Nehal J Wani
* Alan Du
+* Matthew R. Becker
* ossdev07
+* Eli Uriegas
=====================================
CHANGELOG.md
=====================================
@@ -1,4 +1,31 @@
# current developments
+2021-04-12 1.7.3:
+------------------
+
+Enhancements:
+-------------
+
+* Python tar extraction now used as a fallback if libarchive fails
+
+Bug fixes:
+----------
+
+* Fix binsort's mangling of symlinks
+* Fix #71, larger directories fail to extract using libarchive
+* When testing that exceptions are raised or archives containing abs paths, first check that such a "broken" archive was created during test setup... otherwise skip the test.
+* api.create now raises an error correctly if archive creation failed or extension is not supported.
+* Travis CI issue now resolved, mock added as dependency for conda test environments and system dependencies
+* Fixed bug where extract parser cli failed due to not having ``out_folder`` attribute.
+
+Contributors:
+-------------
+
+* @mingwandroid
+* @leej3
+* @beckermr
+* @seemethere
+
+
2020-10-16 1.7.2:
------------------
=====================================
appveyor.yml
=====================================
@@ -1,6 +1,6 @@
environment:
matrix:
- - PYTHON_VERSION: "3.6"
+ - PYTHON_VERSION: "3.9"
- PYTHON_VERSION: "2.7"
install:
=====================================
conda.recipe/meta.yaml
=====================================
@@ -33,11 +33,12 @@ test:
- pytest
- pytest-cov
- pytest-mock
+ - mock
imports:
- conda_package_handling
- conda_package_handling.archive_utils_cy
commands:
- - pytest tests
+ - pytest -v --cov=tests/ --cov-report=xml --color=yes tests/
about:
home: https://github.com/conda/conda-package-handling
summary: Create and extract conda packages of various formats
=====================================
devtools/conda-envs/test_env.yaml
=====================================
@@ -0,0 +1,4 @@
+name: test_env
+dependencies:
+ - anaconda-client
+ - conda-build
=====================================
src/conda_package_handling/_version.py
=====================================
@@ -23,9 +23,9 @@ def get_keywords():
# 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: 1.7.2)"
- git_full = "29b05daaa51ff8c790fa31c401ce372f3a68514a"
- git_date = "2020-10-16 19:02:10 +0200"
+ git_refnames = " (HEAD -> master, tag: 1.7.3)"
+ git_full = "3a8c263f86b2d8b2095684e5b9b787609b0e1b34"
+ git_date = "2021-04-12 11:49:45 +0200"
keywords = {"refnames": git_refnames, "full": git_full, "date": git_date}
return keywords
=====================================
src/conda_package_handling/api.py
=====================================
@@ -76,14 +76,21 @@ def create(prefix, file_list, out_fn, out_folder=None, **kw):
except:
raise
+ out = None
for ext in SUPPORTED_EXTENSIONS:
if out_fn.endswith(ext):
try:
out = SUPPORTED_EXTENSIONS[ext].create(prefix, file_list, out_fn, out_folder, **kw)
- except:
+ break
+ except Exception as err:
# don't leave broken files around
- if _os.path.isfile(out):
+ if out and _os.path.isfile(out):
_rm_rf(out)
+ raise err
+ else:
+ raise ValueError("Didn't recognize extension for file '{}'. Supported extensions are: {}"
+ .format(fn, list(SUPPORTED_EXTENSIONS.keys())))
+
return out
=====================================
src/conda_package_handling/archive_utils_c.c
=====================================
@@ -134,7 +134,7 @@ static int copy_data(struct archive *ar, struct archive *aw)
return (ARCHIVE_OK);
if (r < ARCHIVE_OK)
return (r);
- r = archive_write_data_block(aw, buff, size, (int)offset);
+ r = archive_write_data_block(aw, buff, size, (size_t)offset);
if (r < ARCHIVE_OK) {
return (r);
}
=====================================
src/conda_package_handling/cli.py
=====================================
@@ -73,7 +73,7 @@ def parse_args(parse_this=None):
def main(args=None):
args = parse_args(args)
- if args.out_folder:
+ if hasattr(args, "out_folder") and args.out_folder:
args.out_folder = os.path.abspath(os.path.normpath(os.path.expanduser(args.out_folder))) + os.sep
if args.subparser_name in ('extract', 'x'):
if args.info:
=====================================
src/conda_package_handling/tarball.py
=====================================
@@ -5,6 +5,7 @@ import subprocess
import sys
import tarfile
from tempfile import NamedTemporaryFile
+import logging
try:
from . import archive_utils
@@ -16,6 +17,7 @@ from . import utils
from .interface import AbstractBaseFormat
from .exceptions import CaseInsensitiveFileSystemError, InvalidArchiveError
+LOG = logging.getLogger(__file__)
def _sort_file_order(prefix, files):
"""Sort by filesize or by binsort, to optimize compression"""
@@ -34,7 +36,6 @@ def _sort_file_order(prefix, files):
else:
info_order = 1 + abs(hash(ext)) % (10 ** 8)
return info_order, fsize
-
binsort = os.path.join(sys.prefix, 'bin', 'binsort')
if os.path.exists(binsort):
with NamedTemporaryFile(mode='w', suffix='.filelist', delete=False) as fl:
@@ -49,6 +50,15 @@ def _sort_file_order(prefix, files):
files_list = [f.split(prefix + os.sep, 1)[-1]
for f in files_list]
os.unlink(fl.name)
+ # Binsort does not handle symlinks gracefully. It will follow them. We must correct that.
+ s1 = set(files)
+ s2 = set(files_list)
+ followed = s2 - s1
+ for f in followed:
+ files_list.remove(f)
+ s2 = set(files_list)
+ if len(s1) > len(s2):
+ files_list.extend(s1 - s2)
else:
files_list = list(f for f in sorted(files, key=order))
return files_list
@@ -132,7 +142,14 @@ class CondaTarBZ2(AbstractBaseFormat):
fn = os.path.normpath(os.path.join(os.getcwd(), fn))
if libarchive_enabled:
- _tar_xf(fn, dest_dir)
+ try:
+ _tar_xf(fn, dest_dir)
+ except InvalidArchiveError:
+ LOG.warning(
+ "Failed extraction with libarchive... falling back to python implementation"
+ )
+ _tar_xf_no_libarchive(fn, dest_dir)
+
else:
_tar_xf_no_libarchive(fn, dest_dir)
=====================================
tests/test_api.py
=====================================
@@ -188,6 +188,10 @@ def test_secure_refusal_to_extract_abs_paths(testing_workdir):
with tarfile.open('pinkie.tar.bz2', 'w:bz2') as tf:
open('thebrain', 'w').close()
tf.add(os.path.join(testing_workdir, 'thebrain'), '/naughty/abs_path')
+ try:
+ tf.getmember('/naughty/abs_path')
+ except KeyError:
+ pytest.skip("Tar implementation does not generate unsafe paths in archive.")
with pytest.raises(api.InvalidArchiveError):
api.extract('pinkie.tar.bz2')
View it on GitLab: https://salsa.debian.org/med-team/conda-package-handling/-/commit/7ca4d69c05c0858121fb0a22080da3968cc867f3
--
View it on GitLab: https://salsa.debian.org/med-team/conda-package-handling/-/commit/7ca4d69c05c0858121fb0a22080da3968cc867f3
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