[repo-helper] Configuration Update

.bumpversion.cfg

@@ -9,14 +9,17 @@ replace = : str = "{new_version}"
 
 [bumpversion:file:README.rst]
 
-[bumpversion:file:__pkginfo__.py]
-
 [bumpversion:file:doc-source/index.rst]
 
 [bumpversion:file:pyproject.toml]
 
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
 [bumpversion:file:repo_helper.yml]
 
 [bumpversion:file:pymassspec_plot/__init__.py]
 search = : str = "{current_version}"
 replace = : str = "{new_version}"
+
+[bumpversion:file:.github/workflows/conda_ci.yml]

.github/milestones.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+# stdlib
+import os
+import sys
+
+# 3rd party
+from github3 import GitHub
+from github3.repos import Repository
+from packaging.version import InvalidVersion, Version
+
+latest_tag = os.environ["GITHUB_REF_NAME"]
+
+try:
+	current_version = Version(latest_tag)
+except InvalidVersion:
+	sys.exit()
+
+gh: GitHub = GitHub(token=os.environ["GITHUB_TOKEN"])
+repo: Repository = gh.repository(*os.environ["GITHUB_REPOSITORY"].split('/', 1))
+
+for milestone in repo.milestones(state="open"):
+	try:
+		milestone_version = Version(milestone.title)
+	except InvalidVersion:
+		continue
+	if milestone_version == current_version:
+		sys.exit(not milestone.update(state="closed"))

.github/stale.yml

@@ -7,7 +7,7 @@ daysUntilStale: 180
 
 # Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
 # Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
-daysUntilClose: 180
+daysUntilClose: false
 
 # Only issues or pull requests with all of these labels are check if stale. Defaults to `[]` (disabled)
 onlyLabels: []
@@ -28,13 +28,13 @@ exemptMilestones: false
 exemptAssignees: false
 
 # Label to use when marking as stale
-staleLabel: wontfix
+staleLabel: stale
 
 # Comment to post when marking as stale. Set to `false` to disable
-markComment: >
-  This issue has been automatically marked as stale because it has not had
-  recent activity. It will be closed if no further activity occurs. Thank you
-  for your contributions.
+markComment: false
+#  This issue has been automatically marked as stale because it has not had
+#  recent activity. It will be closed if no further activity occurs. Thank you
+#  for your contributions.
 
 # Comment to post when removing the stale label.
 # unmarkComment: >

.github/workflows/conda_ci.yml

@@ -12,7 +12,10 @@ permissions:
 jobs:
   tests:
     name: "Conda"
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-18.04
+    defaults:
+      run:
+        shell: bash -l {0}
 
     steps:
       - name: Checkout 🛎️
@@ -23,25 +26,41 @@ jobs:
         with:
           python-version: "3.8"
 
+      - name: Setup Conda
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: env
+          conda-build-version: 3.21.0
+
       - name: Install dependencies 🔧
         run: |
           python -VV
           python -m site
           python -m pip install --upgrade pip setuptools wheel
-          python -m pip install --upgrade repo_helper
+          python -m pip install --upgrade "whey-conda" "whey"
           # $CONDA is an environment variable pointing to the root of the miniconda directory
-          $CONDA/bin/conda update -q conda
-          $CONDA/bin/conda install conda-build=3.21.0
-
+          $CONDA/bin/conda update -n base conda
           $CONDA/bin/conda config --add channels bioconda
           $CONDA/bin/conda config --add channels conda-forge
           $CONDA/bin/conda config --add channels domdfcoding
 
-      - name: "Build and install package"
+      - name: "Build and index channel"
         run: |
-          # This mess is only necessary because conda won't fix it themselves
-          # https://github.com/conda/conda/issues/1884
-
-          python -m repo_helper build --conda --out-dir conda-bld/noarch
+          python -m whey --builder whey_conda --out-dir conda-bld/noarch
           $CONDA/bin/conda index ./conda-bld || exit 1
-          $CONDA/bin/conda install -c file://$(pwd)/conda-bld pymassspec-plot -y || exit 1
+
+      - name: "Search for package"
+        run: |
+          $CONDA/bin/conda search -c file://$(pwd)/conda-bld pymassspec-plot
+          $CONDA/bin/conda search -c file://$(pwd)/conda-bld --override-channels pymassspec-plot
+
+      - name: "Install package"
+        run: |
+          $CONDA/bin/conda install -c file://$(pwd)/conda-bld pymassspec-plot=0.0.0=py_1 -y || exit 1
+
+      - name: "Run Tests"
+        run: |
+          rm -rf pymassspec_plot
+          $CONDA/bin/conda install pytest coincidence || exit 1
+          pip install -r tests/requirements.txt
+          pytest tests/

.github/workflows/docs_test_action.yml

@@ -2,7 +2,12 @@
 ---
 name: "Docs Check"
 on:
-  - push
+  push:
+    branches-ignore:
+      - 'repo-helper-update'
+      - 'pre-commit-ci-update-config'
+      - 'imgbot'
+  pull_request:
 
 permissions:
   contents: read
@@ -12,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout 🛎️
-        uses: "actions/checkout@v1"
+        uses: "actions/checkout@v2"
 
       - name: Check for changed files
         uses: dorny/paths-filter@v2

.github/workflows/flake8.yml

@@ -4,6 +4,11 @@ name: Flake8
 
 on:
   push:
+    branches-ignore:
+      - 'repo-helper-update'
+      - 'pre-commit-ci-update-config'
+      - 'imgbot'
+  pull_request:
 
 permissions:
   contents: read

.github/workflows/mypy.yml

@@ -4,6 +4,11 @@ name: mypy
 
 on:
   push:
+    branches-ignore:
+      - 'repo-helper-update'
+      - 'pre-commit-ci-update-config'
+      - 'imgbot'
+  pull_request:
 
 permissions:
   contents: read

.github/workflows/octocheese.yml

@@ -3,10 +3,8 @@
 
 name: "GitHub Releases"
 on:
-  push:
-    branches: ["master"]
   schedule:
-    - cron: 0 12 * * 2,4,6
+    - cron: 0 12 * * *
 
 jobs:
   Run:

.github/workflows/python_ci.yml

@@ -4,9 +4,16 @@ name: Windows
 
 on:
   push:
+    branches-ignore:
+      - 'repo-helper-update'
+      - 'pre-commit-ci-update-config'
+      - 'imgbot'
+
+  pull_request:
 
 permissions:
   actions: write
+  issues: write
   contents: read
 
 jobs:
@@ -15,7 +22,7 @@ jobs:
     runs-on: "windows-2019"
     continue-on-error: ${{ matrix.config.experimental }}
     env:
-      USING_COVERAGE: '3.6,3.7,3.8,3.9,3.10.0-beta.1'
+      USING_COVERAGE: '3.6,3.7,3.8,3.9,3.10'
 
     strategy:
       fail-fast: False
@@ -25,7 +32,7 @@ jobs:
           - {python-version: "3.7", testenvs: "py37,build", experimental: False}
           - {python-version: "3.8", testenvs: "py38,build", experimental: False}
           - {python-version: "3.9", testenvs: "py39,build", experimental: False}
-          - {python-version: "3.10.0-beta.1", testenvs: "py310-dev,build", experimental: True}
+          - {python-version: "3.10", testenvs: "py310-dev,build", experimental: True}
 
     steps:
       - name: Checkout 🛎️