Merge pull request #173 from MannLabs/development

Development
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.
-