Merge pull request #137 from dwhswenson/fix-pkg-resources

Get tests passing again

Author: dwhswenson

.github/workflows/autorelease-default-env.sh

@@ -1,4 +1,6 @@
-INSTALL_AUTORELEASE="python -m pip install autorelease==0.2.6"
+# Vendored from Autorelease 0.7.0
+# Update by updating Autorelease and running `autorelease vendor actions`
+INSTALL_AUTORELEASE="python -m pip install autorelease==0.7.0"
 if [ -f autorelease-env.sh ]; then
     source autorelease-env.sh
 fi

.github/workflows/autorelease-deploy.yml

@@ -1,33 +1,29 @@
-name: Autorelease
+# Vendored from Autorelease 0.7.0
+# Update by updating Autorelease and running `autorelease vendor actions`
+name: "Autorelease Deploy"
 on:
   release:
     types: [published]
 
 jobs:
   deploy_pypi:
+    if: ${{ github.repository == 'dwhswenson/contact_map' }}
     runs-on: ubuntu-latest
     name: "Deploy to PyPI"
+    permissions:
+      id-token: write
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v5
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.x"
-      - run: |  # TODO: move this to an action
-          source ./.github/workflows/autorelease-default-env.sh
-          if [ -f "autorelease-env.sh" ]; then
-            cat autorelease-env.sh >> $GITHUB_ENV
-          fi
-          eval $INSTALL_AUTORELEASE
-        name: "Install autorelease"
       - run: |
-          python -m pip install twine wheel
+          python -m pip install twine wheel build
         name: "Install release tools"
       - run: |
-          python setup.py sdist bdist_wheel
+          python -m build --sdist --wheel
           twine check dist/*
         name: "Build and check package"
-      - uses: pypa/gh-action-pypi-publish@master
-        with:
-          password: ${{ secrets.pypi_password }}
+      - uses: pypa/gh-action-pypi-publish@release/v1
         name: "Deploy to pypi"
 

.github/workflows/autorelease-gh-rel.yml

@@ -1,24 +1,32 @@
-name: Autorelease
+# Vendored from Autorelease 0.7.0
+# Update by updating Autorelease and running `autorelease vendor actions`
+name: "Autorelease Release"
 on:
   push:
     branches:
+      # TODO: this should come from yaml conf
       - stable
 
 jobs:
   release-gh:
+    if: ${{ github.repository == 'dwhswenson/contact_map' }}
     runs-on: ubuntu-latest
     name: "Cut release"
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: "3.7"
+          python-version: "3.x"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
           if [ -f "autorelease-env.sh" ]; then
             cat autorelease-env.sh >> $GITHUB_ENV
           fi
-          eval $INSTALL_AUTORELEASE
+          if [ -f "./.autorelease/install-autorelease" ]; then
+            source ./.autorelease/install-autorelease
+          else
+            eval $INSTALL_AUTORELEASE
+          fi
         name: "Install autorelease"
       - run: |
           VERSION=`python setup.py --version`
@@ -27,3 +35,4 @@ jobs:
           autorelease-release --project $PROJECT --version $VERSION --token $AUTORELEASE_TOKEN
         env:
           AUTORELEASE_TOKEN: ${{ secrets.AUTORELEASE_TOKEN }}
+        name: "Cut release"

.github/workflows/autorelease-prep.yml

@@ -1,7 +1,10 @@
-name: "Autorelease"
+# Vendored from Autorelease 0.7.0
+# Update by updating Autorelease and running `autorelease vendor actions`
+name: "Autorelease testpypi"
 on:
   pull_request:
     branches:
+      # TODO: this should come from yaml conf
       - stable
 
 defaults:
@@ -10,19 +13,26 @@ defaults:
 
 jobs:
   deploy_testpypi:
+    permissions:
+      id-token: write
+    if: ${{ github.repository == 'dwhswenson/contact_map' }}
     runs-on: ubuntu-latest
     name: "Deployment test"
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
           if [ -f "autorelease-env.sh" ]; then
             cat autorelease-env.sh >> $GITHUB_ENV
           fi
-          eval $INSTALL_AUTORELEASE
+          if [ -f "./.autorelease/install-autorelease" ]; then
+            source ./.autorelease/install-autorelease
+          else
+            eval $INSTALL_AUTORELEASE
+          fi
         name: "Install autorelease"
       - run: |
           python -m pip install twine wheel
@@ -35,26 +45,36 @@ jobs:
           python setup.py sdist bdist_wheel
           twine check dist/*
         name: "Build and check package"
-      - uses: pypa/gh-action-pypi-publish@master
+      - uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          password: ${{ secrets.testpypi_password }}
           repository_url: https://test.pypi.org/legacy/
         name: "Deploy to testpypi"
   test_testpypi:
+    if: ${{ github.repository == 'dwhswenson/contact_map' }}
     runs-on: ubuntu-latest
     name: "Test deployed"
     needs: deploy_testpypi
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: "3.x"
       - run: |  # TODO: move this to an action
           source ./.github/workflows/autorelease-default-env.sh
           if [ -f "autorelease-env.sh" ]; then
             cat autorelease-env.sh >> $GITHUB_ENV
           fi
-          eval $INSTALL_AUTORELEASE
+          if [ -f "./.autorelease/install-autorelease" ]; then
+            source ./.autorelease/install-autorelease
+          else
+            eval $INSTALL_AUTORELEASE
+          fi
         name: "Install autorelease"
-      - run: test-testpypi
-
+      - name: "Install testpypi version"
+        run: install-testpypi
+      - name: "Test testpypi version"
+        run: |
+          if [ -f "autorelease-env.sh" ]; then
+            cat autorelease-env.sh >> $GITHUB_ENV
+          fi
+          test-testpypi

.github/workflows/unit-tests.yml

@@ -23,31 +23,30 @@ jobs:
     strategy:
       matrix:
         CONDA_PY:
-          - "3.13"
           - "3.12"
-          - "3.11"
+          - "3.13"
+          - "3.14"
         OS: ["ubuntu"]
         MDTRAJ: ["mdtraj-release"]
         INSTALL_WITH: ["pip"]
         include:
-          - CONDA_PY: "3.13"
+          - CONDA_PY: "3.14"
             OS: "ubuntu"
             MDTRAJ: "mdtraj-dev"
             INSTALL_WITH: "pip"
-          - CONDA_PY: "3.13"
+          - CONDA_PY: "3.14"
             OS: "windows"
             MDTRAJ: "mdtraj-release"
             INSTALL_WITH: "conda"
-          - CONDA_PY: "3.11"
+          - CONDA_PY: "3.12"
             OS: "windows"
             MDTRAJ: "mdtraj-release"
             INSTALL_WITH: "conda"
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
-      - uses: actions/setup-python@v2
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true

contact_map/tests/utils.py

@@ -1,5 +1,5 @@
 import os
-from pkg_resources import resource_filename
+from importlib.resources import files
 
 # pylint: disable=unused-import
 
@@ -8,7 +8,7 @@
 import pytest
 
 def find_testfile(fname):
-    return resource_filename('contact_map', os.path.join('tests', fname))
+    return os.fspath(files(__package__).joinpath(fname))
 
 def zero_to_nan(input_arr):
     arr = input_arr.copy()

docs/conf.py

@@ -19,8 +19,10 @@
 import os
 import sys
 import shutil
+from configparser import ConfigParser
+from importlib.metadata import PackageNotFoundError, version as package_version
+
 import sphinx_rtd_theme
-import pkg_resources
 import packaging.version
 # sys.path.insert(0, os.path.abspath('.'))
 #sys.path.insert(0, os.path.abspath('../contact_map/'))
@@ -41,7 +43,16 @@
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
-release = pkg_resources.get_distribution('contact_map').version
+def get_release():
+    try:
+        return package_version('contact_map')
+    except PackageNotFoundError:
+        conf = ConfigParser()
+        conf.read(os.path.abspath('../setup.cfg'))
+        return conf.get('metadata', 'version')
+
+
+release = get_release()
 version = packaging.version.Version(release).base_version
 
 # The short X.Y version.