Release? (#306)

* added new translation function * new orfs method for Seq based on three_frame_orfs function * new orfs_to_features method for Dseqrecord * new extract_from_text functions that also returns the intervening text between sequences * bugfix orfs for Seq and Dsecrecord * added crispr tests * added pairwise for older Python versions * older type hint * Deploying to gh-pages from @ da3e7e9 🚀 * Deploying to gh-pages from @ 5be4f9d 🚀 * Deploying to gh-pages from @ b37a17c 🚀 * Deploying to gh-pages from @ 11aae3c 🚀 * Deploying to gh-pages from @ 0f95223 🚀 * try to build docs locally on gh-pages * try to build gh pages * try to build gh pages * fix * added sphinx ext * Deploying to gh-pages from @ bc08a36 🚀 * try fix docs * build docs * clean * redirect docs badge to action * redirect docs badge to action * fix readme links * fix readme * fix * try to fix test error * fix bug that recognized parts of re enzyme names as other enzymes * added comment with number of enzymes * changed number of expected enzymes to the correct number 621 * more informative error msg * closes #216 (2) * closes #196 * vscode and poetry settings added * fix test * add locations_overlap to utils * Issue 238 (#239) * closes #238 * fix notebook * closes #240 * atomically write default config * optimisation for #237 * fix python 3.8 typing * include neb calculator and its tests * fix design and add tests * example commit for #176 * Documentation notebooks 2 (#272) * Documentation notebooks (#271) * added documentation for dseq.py * fixed docs for Dseq.py * fixed docs for Dseq.py * add hook * fix exclusions and run hook * strip outputs of Dseq.ipynb * update Dseq notebook * placed notebooks in docs * added looped and shifted methods in Dseq docs * added docs for importing files using pydna * added some Dseqrecord docs * added docs+examples for Dseq_Features * added origin spanning feats and removing feats for Dseq_Features * some comments and todos * added restriction page * updated Importing_Seq page * updated Dseq_Feature Page w/examples * added restrict+ligate notebook * added some PCR notes * added examples, prints * added tm and design * fixed tm_default docs * added gibson assembly * some comments on current progress * gibson * fixed comments, added gibson example and CRISPR * added Restriction example * added Gibson example * closes #256 * run pre-commit * alternative example for gibson * gibson updated example * modified crispr * modified crispr * feedback changes for #260 * best practices for qualifiers --------- Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com> Co-authored-by: Pei-Lun Xie <31442380+JeffXiePL@users.noreply.github.com> * remove unnecessary file * remove dir exclusions * exclude test notebooks --------- Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com> Co-authored-by: Pei-Lun Xie <31442380+JeffXiePL@users.noreply.github.com> * update contribution guidelines (#274) * update CI action to enforce hooks (#277) * update CI action to enforce hooks * update action * update: Added google badge to all notebooks issue #266 (#275) * fourth trt * final file added * update: added installation of pydna * added seguid stamp to Genbank sequence files * fix test sequence file * dependabot monthly * New CRISPR example notebook (#260) (#284) * fourth trt * final file added * update: added installation of pydna * update: added CRIPSR examples in notebooks issue #259 * update: added google badge issue #266 * Polished Example CRISPR notebook --------- Co-authored-by: Manuel Lera-Ramirez <manulera14@gmail.com> * Updated notebooks (#295) * updated example_restriction (#285) Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com> * small fixes (#294) * allow run all on notebooks that have pip install for google colab --------- Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com> * progress towards #261 * WIP * remove code image from README for #261 * more README updates + make requirements.txt * add requirements file * fix configuration * typing for PrettyTable * typing for codon dicts * typing for Seq * typing for FakeSeq * typing for Genbank * typing for sequence_picker module * typing for common_sub_strings module * typing for Assembly.__init__ and Assembly.__repr__ * Bump pillow from 10.3.0 to 10.4.0 Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.3.0 to 10.4.0. - [Release notes](https://github.com/python-pillow/Pillow/releases) - [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst) - [Commits](python-pillow/Pillow@10.3.0...10.4.0) --- updated-dependencies: - dependency-name: pillow dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Bump autopep8 from 2.1.0 to 2.3.1 Bumps [autopep8](https://github.com/hhatto/autopep8) from 2.1.0 to 2.3.1. - [Release notes](https://github.com/hhatto/autopep8/releases) - [Commits](hhatto/autopep8@v2.1.0...v2.3.1) --- updated-dependencies: - dependency-name: autopep8 dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Bump black from 24.4.2 to 24.8.0 Bumps [black](https://github.com/psf/black) from 24.4.2 to 24.8.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](psf/black@24.4.2...24.8.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * Bump sphinx-rtd-theme from 2.0.0 to 3.0.0 Bumps [sphinx-rtd-theme](https://github.com/readthedocs/sphinx_rtd_theme) from 2.0.0 to 3.0.0. - [Changelog](https://github.com/readthedocs/sphinx_rtd_theme/blob/master/docs/changelog.rst) - [Commits](readthedocs/sphinx_rtd_theme@2.0.0...3.0.0) --- updated-dependencies: - dependency-name: sphinx-rtd-theme dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <support@github.com> * Bump prettytable from 3.10.0 to 3.11.0 Bumps [prettytable](https://github.com/jazzband/prettytable) from 3.10.0 to 3.11.0. - [Release notes](https://github.com/jazzband/prettytable/releases) - [Changelog](https://github.com/jazzband/prettytable/blob/main/CHANGELOG.md) - [Commits](prettytable/prettytable@3.10.0...3.11.0) --- updated-dependencies: - dependency-name: prettytable dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <support@github.com> * closes #261 (#297) * tests for #281 #279, add type to pcr (#298) * update codecov action for #242 * Issue 270 (#301) * closes #270 * closes #269 by adding an example notebook + extra tests * closes #288, includes the graphics in docs notebook * added example.ipynb to tests folder * removed example.ipynb * deal with Tm = 0 * fix notebook export related to #279 * New docs (#304) * new docs * update action * update action * fix typo in action * update README + closes #305 * improve docs * document how docs work * fix autogen_docs.sh * fix crispr docstring * Fix link in README (#310) * Fix action (#311) * fix action * fix action --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: BjornFJohansson <bjornjobb@gmail.com> Co-authored-by: BjornFJohansson <bjorn_johansson@bio.uminho.pt> Co-authored-by: Pei-Lun Xie <peilunx.jeff@gmail.com> Co-authored-by: Jerry Xu <jxu@hexagonbio.com> Co-authored-by: Pei-Lun Xie <31442380+JeffXiePL@users.noreply.github.com> Co-authored-by: Lucas Levassor <70581528+hiyama341@users.noreply.github.com> Co-authored-by: Kawin <krayon.py@gmail.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Daniel García Ruano <daniel.garcia-ruano@u-bordeaux.fr>
BjornFJohansson · Oct 24, 2024 · 0a9fe6e · 0a9fe6e
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Showing 171 changed files with 89,046 additions and 11,105 deletions.
diff --git a/.buildinfo b/.buildinfo
@@ -0,0 +1,4 @@
+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: e1ad02ce3592def18a437f1884177507
+tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/.git_archival.json b/.git_archival.json
diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml
@@ -0,0 +1,53 @@
+on: [push, pull_request]
+
+name: "Documentation Status"
+
+permissions:
+  contents: write
+
+jobs:
+  build-and-publish:
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+
+    timeout-minutes: 10
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+
+    - name: Session information
+      run: |
+        python --version
+
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+      with:
+        virtualenvs.prefer-active-python: true
+
+    - name: 🔩 list Poetry settings
+      run: poetry config --list
+
+    - name: 🔩 Install with Poetry
+      run: poetry install --all-extras --with docs
+
+    - name: Build documentation
+      run: |
+        cd docs
+        poetry run bash autogen_docs.sh
+        poetry run make html
+
+    - name: Deploy to GitHub pages 🚀
+      # Deploy only when master changes
+      if: github.ref == 'refs/heads/master' && github.event_name == 'push'
+      uses: JamesIves/github-pages-deploy-action@v4.6.0
+      with:
+        clean: false
+        branch: gh-pages
+        folder: docs/_build/html
diff --git a/.github/workflows/pydna_test_and_coverage_workflow.yml b/.github/workflows/pydna_test_and_coverage_workflow.yml
@@ -2,32 +2,32 @@ name: Tests & Coverage
 on:
   push:
     branches:
-      - '**'
-      - '!master'   # excludes master branch
-      - '!testpypi' # excludes testpypi branch
+      - "**"
+      - "!master" # excludes master branch
+      - "!testpypi" # excludes testpypi branch
     tags-ignore:
-      - '*.*'
+      - "*.*"
   pull_request: {}
 jobs:
   build:
     name: Test (${{ matrix.python-version }}, ${{ matrix.os }})
     strategy:
       fail-fast: false
       matrix:
-        os: [ 'macos-latest', 'windows-latest' ]
+        os: ["macos-latest", "windows-latest"]
         python-version: ["3.12", "3.11", "3.10", "3.9", "3.8"]
         include:
-        - os: ubuntu-latest
-          python-version: "3.8"
-          codecov: true
-        - os: ubuntu-latest
-          python-version: "3.9"
-        - os: ubuntu-latest
-          python-version: "3.10"
-        - os: ubuntu-latest
-          python-version: "3.11"
-        - os: ubuntu-latest
-          python-version: "3.12"
+          - os: ubuntu-latest
+            python-version: "3.8"
+            codecov: true
+          - os: ubuntu-latest
+            python-version: "3.9"
+          - os: ubuntu-latest
+            python-version: "3.10"
+          - os: ubuntu-latest
+            python-version: "3.11"
+          - os: ubuntu-latest
+            python-version: "3.12"
     defaults:
       run:
         shell: bash
@@ -50,7 +50,7 @@ jobs:
       - name: Install Poetry
         uses: snok/install-poetry@v1
         with:
-           virtualenvs.prefer-active-python: true
+          virtualenvs.prefer-active-python: true
 
       - name: 🔩 list Poetry settings
         run: poetry config --list
@@ -61,9 +61,36 @@ jobs:
       - name: 🔎 poetry run python run_test.py
         run: poetry run python run_test.py
 
+      # Enforce pre-commit hooks ===========================
+      - name: Get changed files
+        if: (matrix.codecov)
+        id: changed-files
+        uses: tj-actions/changed-files@v45
+        with:
+          since_last_remote_commit: true
+
+      - uses: actions/cache@v4
+        if: (matrix.codecov)
+        id: cache-precommit
+        with:
+          path: ~/.cache/pre-commit
+          key: ${{ runner.os }}-precommit-hooks-v2-${{ hashFiles('**/.pre-commit-config.yaml') }}
+
+      - name: Installing pre-commit hooks (cached)
+        if: (matrix.codecov) && (steps.cache-precommit.outputs.cache-hit != 'true')
+        run: poetry run pre-commit install --install-hooks
+
+      - name: Run style checking via pre-commit
+        if: (matrix.codecov && steps.changed-files.outputs.all_changed_files)
+        run: |
+          echo "Changed files:"
+          echo "${{ steps.changed-files.outputs.all_changed_files }}" | tr ' ' '\n'
+          poetry run pre-commit run --files ${{ steps.changed-files.outputs.all_changed_files }}
+
+      # ======================================================
       - name: 🔼 Upload coverage to Codecov
         if: (matrix.codecov)
-        uses: codecov/codecov-action@v1.0.13
+        uses: codecov/codecov-action@v4
         with:
           file: ./coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}

diff --git a/.gitignore b/.gitignore
@@ -36,6 +36,7 @@ var/
 *.egg-info/
 .installed.cfg
 *.egg
+.venv/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -65,6 +66,8 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/markdown_notebooks
+docs/modules/
 
 # PyBuilder
 target/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,20 +2,57 @@ repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
   rev: v4.5.0
   hooks:
+  # Prevent committing to the master branch
   - id: no-commit-to-branch
     args: [--branch, master]
+  # Format yaml files
   - id: check-yaml
+  # Fix end-of-file issues
   - id: end-of-file-fixer
+  # Fix trailing whitespace
   - id: trailing-whitespace
+  # Prevent debug statements
   - id: debug-statements
   - id: fix-encoding-pragma
   - id: mixed-line-ending
+# Code formatting
 - repo: https://github.com/ambv/black
   rev: 24.2.0
   hooks:
   - id: black
+# Further linting (e.g. module imported but not used)
 - repo: https://github.com/PyCQA/flake8
   rev: 7.0.0
   hooks:
   - id: flake8
-exclude: scripts/|docs/|tests/
+# Verify that requirements.txt is up to date with poetry dependencies every commit
+- repo: https://github.com/python-poetry/poetry
+  rev: 1.8.3
+  hooks:
+    - id: poetry-export
+      args: [
+        "-f",
+        "requirements.txt",
+        "--output",
+        "requirements.txt",
+        "--with",
+        "dev",
+        "--with",
+        "test",
+        "--with",
+        "docs",
+        "-E",
+        "clipboard download express gel",
+      ]
+      files: 'requirements.txt'
+# Remove metadata from jupyter notebooks. This will always be triggered when you commit a change in a notebook.
+# Simply do `git add` and commit again.
+- repo: local
+  hooks:
+    - id: nbstripout
+      name: nbstripout with keep-output
+      entry: |
+        python -m nbstripout --keep-output $@
+      language: system
+      files: \.ipynb$
+      exclude: tests/
diff --git a/.readthedocs.yml b/.readthedocs.yml
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
@@ -0,0 +1,8 @@
+{
+    "recommendations": [
+        "ms-python.black-formatter",
+        "ms-python.flake8",
+        "ms-python.python",
+        "ms-python.vscode-pylance",
+    ]
+}
diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -0,0 +1,15 @@
+{
+    "files.exclude": {
+        "**/.git": true,
+        "**/.svn": true,
+        "**/.hg": true,
+        "**/CVS": true,
+        "**/.DS_Store": true,
+        "**/*.pyc": true,
+        "**/__pycache__": true
+    },
+    // Set flake8 path
+    "flake8.path": [".venv/bin/flake8"],
+    "black-formatter.path": [".venv/bin/black"],
+    "python.defaultInterpreterPath": ".venv/bin/python",
+}