Merge pull request #173 from MannLabs/development

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MannLabs · May 29, 2024 · 2ecc4ce · 2ecc4ce
2 parents 0222f2e + eb4f1e7
commit 2ecc4ce
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Showing 159 changed files with 1,568 additions and 1,551 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,9 +1,9 @@
 [bumpversion]
-current_version = 1.1.9
+current_version = 1.2.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?
-serialize = 
+serialize =
 	{major}.{minor}.{patch}
 	{major}.{minor}.{patch}
 
@@ -15,8 +15,6 @@ serialize =
 
 [bumpversion:file:./docs/conf.py]
 
-[bumpversion:file:./settings.ini]
-
 [bumpversion:file:./release/one_click_linux_gui/control]
 
 [bumpversion:file:./release/one_click_linux_gui/create_installer_linux.sh]

diff --git a/.devcontainer.json b/.devcontainer.json
diff --git a/.github/workflows/_run_tests.yml b/.github/workflows/_run_tests.yml
@@ -0,0 +1,46 @@
+# reusable workflow to run all tests
+name: run-tests
+
+on:
+  workflow_call:
+    inputs:
+      os:
+        required: true
+        type: string
+      python-version:
+        required: true
+        type: string
+      install-script:
+        required: true
+        type: string
+jobs:
+  pre-commit:
+    runs-on: ${{ inputs.os }}
+    steps:
+    - uses: actions/checkout@v3
+    - uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniconda-version: "latest"
+        auto-update-conda: true
+        python-version: ${{ inputs.python-version }}
+    - name: Conda info
+      shell: bash -l {0}
+      run: conda info
+    - name: Perform pip installation with all stable dependencies
+      shell: bash -l {0}
+      run: |
+        cd misc
+        . ./${{ inputs.install-script }}
+    - name: Install additional dependencies required for testing
+      shell: bash -l {0}
+      run: |
+        conda activate peptdeep
+        pip install pytest nbmake==1.5.3
+        conda deactivate
+    - name: nbs_unitests
+      shell: bash -l {0}
+      run: |
+        conda activate peptdeep
+        cd tests
+        . ./run_tests.sh
+        conda deactivate
diff --git a/.github/workflows/branch-checks.yaml b/.github/workflows/branch-checks.yaml
@@ -0,0 +1,25 @@
+# checks to run on branches for each pull request
+name: branch-checks
+
+on:
+  pull_request:
+
+jobs:
+  pre-commit:
+    name: Run all pre-commit hooks
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - uses: actions/setup-python@v3
+    - uses: pre-commit/[email protected]
+  # For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
+  run-tests-loose:
+    name: Test loose pip installation on ubuntu-latest
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+    uses: ./.github/workflows/_run_tests.yml
+    with:
+      python-version: ${{ matrix.python-version }}
+      os: ${{ matrix.os }}
+      install-script: "loose_pip_install.sh"
diff --git a/.github/workflows/github_action_test_dummy.yml b/.github/workflows/github_action_test_dummy.yml
diff --git a/.github/workflows/pip_installation.yml b/.github/workflows/pip_installation.yml
@@ -1,66 +1,42 @@
+# Perform pip installation and run all tests
+
+# For feature branches, we don't test the full matrix (os x [stable, loose]) in order to save time & resources.
+# On each push to develop, the whole test matrix runs, additionally, its success is mandatory for merging to main.
+# In the (assumed to be rare case) that these full matrix tests fail but the reduced matrix tests passed,
+# we will learn about it latest before pushing to main. The merge that caused the issue can then be identified
+# from the tests that ran on develop.
 on:
   push:
-    branches: [ main ]
-  pull_request:
     branches: [ main, development ]
+  pull_request:
+    branches: [ main ]
   workflow_dispatch:
 
-name: Default installation and tests
+name: Pip installation and tests
 
 jobs:
   stable_installation:
     name: Test stable pip installation on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macOS-latest, windows-latest]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-      - name: Test pip installation with all stable dependencies
-        shell: bash -l {0}
-        run: |
-          cd misc
-          . ./stable_pip_install.sh
-      - name: Unittests
-        shell: bash -l {0}
-        run: |
-          conda activate peptdeep
-          pip install -U git+https://github.com/mannlabs/alphabase.git@development
-          peptdeep
-          nbdev_test
-          conda deactivate
+        os: [ubuntu-latest, macos-13, windows-latest]
+        # macOS-latest and macos-latest-xlarge use Arm64, resulting in MPS OOM error in peptdeep
+        # os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+    uses: ./.github/workflows/_run_tests.yml
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      install-script: "stable_pip_install.sh"
+
   loose_installation:
     name: Test loose pip installation on ${{ matrix.os }}
-    runs-on: ${{ matrix.os }}
+    # runs-on: ${{ matrix.os }} # See https://github.com/orgs/community/discussions/62320
     strategy:
       matrix:
-        os: [ubuntu-latest, macOS-latest, windows-latest]
-    steps:
-      - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
-        with:
-          auto-update-conda: true
-          python-version: ${{ matrix.python-version }}
-      - name: Conda info
-        shell: bash -l {0}
-        run: conda info
-      - name: Test pip installation with all loose dependencies
-        shell: bash -l {0}
-        run: |
-          cd misc
-          . ./loose_pip_install.sh
-      - name: Unittests
-        shell: bash -l {0}
-        run: |
-          conda activate peptdeep
-          pip install -U git+https://github.com/mannlabs/alphabase.git@development
-          peptdeep
-          nbdev_test
-          conda deactivate
+        os: [ubuntu-latest, macos-13, windows-latest]
+        # os: [ubuntu-latest, macOS-latest, windows-latest, macos-latest-xlarge]
+    uses: ./.github/workflows/_run_tests.yml
+    with:
+      os: ${{ matrix.os }}
+      python-version: ${{ matrix.python-version }}
+      install-script: "loose_pip_install.sh"
diff --git a/.github/workflows/publish_and_release.yml b/.github/workflows/publish_and_release.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -47,7 +47,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -79,7 +79,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -111,7 +111,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -146,7 +146,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -181,7 +181,7 @@ jobs:
         os: [ubuntu-latest, macOS-latest, windows-latest]
     steps:
       - uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

diff --git a/.github/workflows/release_installers.yml b/.github/workflows/release_installers.yml
@@ -11,7 +11,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -44,7 +44,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -76,7 +76,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -108,7 +108,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -140,7 +140,7 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@v3
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

diff --git a/.gitignore b/.gitignore
@@ -143,4 +143,4 @@ _docs*
 # *sidebar.yml
 *_proc*
 # .gitconfig is now autogenerated
-.gitconfig
+.gitconfig
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,14 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v2.3.0
+  hooks:
+    - id: check-yaml
+    - id: end-of-file-fixer
+    - id: trailing-whitespace
+# - repo: https://github.com/astral-sh/ruff-pre-commit
+#   rev: v0.4.0
+#   hooks:
+#     - id: ruff-format
+#     - id: ruff
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -22,4 +22,4 @@ sphinx:
 # # Optionally set the version of Python and requirements required to build your docs
 python:
   install:
-    - requirements: requirements/requirements_development.txt
+    - requirements: requirements/requirements_development.txt
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -29,4 +29,3 @@
 ## Do you want to contribute to the documentation?
 
 * Docs are automatically created from the notebooks in the nbs folder.
-
Original file line number	Diff line number	Diff line change
Expand Up		@@ -29,4 +29,3 @@
		## Do you want to contribute to the documentation?

		* Docs are automatically created from the notebooks in the nbs folder.