Merge branch '4.x'

.dockerignore

@@ -1,5 +1,5 @@
-.git
 .venv
 .ruff_cache
 db
 docs
+tests

.github/ISSUE_TEMPLATE/01-bug_report.yml

@@ -0,0 +1,45 @@
+name: Bug report
+description: Report something that is broken or incorrect
+labels: bug
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
+        detailing how to provide the necessary information for us to reproduce your bug. In brief:
+          * Please provide exact steps how to reproduce the bug in a clean Python environment.
+          * In case it's not clear what's causing this bug, please provide the data or the data generation procedure.
+          * Sometimes it is not possible to share the data, but usually it is possible to replicate problems on publicly
+            available datasets or to share a subset of your data.
+
+  - type: textarea
+    id: report
+    attributes:
+      label: Report
+      description: A clear and concise description of what the bug is.
+    validations:
+      required: true
+
+  - type: textarea
+    id: versions
+    attributes:
+      label: Version information
+      description: |
+        Please paste below the output of
+
+        ```python
+        import session_info
+        session_info.show(html=False, dependencies=True)
+        ```
+      placeholder: |
+        -----
+        dbcan               0.1.dev357+g4e1041c.d20240223
+        session_info        1.0.0
+        -----
+        google              NA
+        sphinxcontrib       NA
+        -----
+        Python 3.10.13 (main, Nov 15 2023, 11:07:58) [Clang 14.0.0 (clang-1400.0.29.202)]
+        macOS-12.7.3-x86_64-i386-64bit
+        -----
+        Session information updated at 2024-02-22 20:12

.github/ISSUE_TEMPLATE/02-feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature request
+description: Propose a new feature for scHub
+labels: enhancement
+body:
+  - type: textarea
+    id: description
+    attributes:
+      label: Description of feature
+      description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered.
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1 @@
+blank_issues_enabled: true

.github/workflows/build.yaml

@@ -0,0 +1,29 @@
+name: Check Build
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  package:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "**/pyproject.toml"
+      - name: Install build dependencies
+        run: python -m pip install --upgrade pip wheel twine build
+      - name: Build package
+        run: python -m build
+      - name: Check package
+        run: twine check --strict dist/*.whl

.github/workflows/docker_pkg.yaml

@@ -0,0 +1,62 @@
+name: publish docker package
+
+# Configures this workflow to run every time a change is pushed to the branch called `release`.
+on:
+  push:
+    branches: ['master']
+
+# Defines two custom environment variables for the workflow. These are used for the Container registry domain, and a name for the Docker image that this workflow builds.
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+
+# There is a single job in this workflow. It's configured to run on the latest available version of Ubuntu.
+jobs:
+  build-and-push-image:
+    runs-on: ubuntu-latest
+    # Sets the permissions granted to the `GITHUB_TOKEN` for the actions in this job.
+    permissions:
+      contents: read
+      packages: write
+      attestations: write
+      id-token: write
+      #
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+      # Uses the `docker/login-action` action to log in to the Container registry registry using the account and password that will publish the packages. Once published, the packages are scoped to the account defined here.
+      - name: Log in to the Container registry
+        uses: docker/login-action@65b78e6e13532edd9afa3aa52ac7964289d1a9c1
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+      # This step uses [docker/metadata-action](https://github.com/docker/metadata-action#about) to extract tags and labels that will be applied to the specified image. The `id` "meta" allows the output of this step to be referenced in a subsequent step. The `images` value provides the base name for the tags and labels.
+      - name: Extract metadata (tags, labels) for Docker
+        id: meta
+        uses: docker/metadata-action@9ec57ed1fcdbf14dcef7dfbe97b2010124a938b7
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          tags: |
+            # minimal
+            type=semver,pattern={{version}}
+      # This step uses the `docker/build-push-action` action to build the image, based on your repository's `Dockerfile`. If the build succeeds, it pushes the image to GitHub Packages.
+      # It uses the `context` parameter to define the build's context as the set of files located in the specified path. For more information, see "[Usage](https://github.com/docker/build-push-action#usage)" in the README of the `docker/build-push-action` repository.
+      # It uses the `tags` and `labels` parameters to tag and label the image with the output from the "meta" step.
+      - name: Build and push Docker image
+        id: push
+        uses: docker/build-push-action@f2a1d5e99d037542a71f64918e516c093c6f3fc4
+        with:
+          context: .
+          push: false
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+
+      # This step generates an artifact attestation for the image, which is an unforgeable statement about where and how it was built. It increases supply chain security for people who consume the image. For more information, see "[AUTOTITLE](/actions/security-guides/using-artifact-attestations-to-establish-provenance-for-builds)."
+      - name: Generate artifact attestation
+        uses: actions/attest-build-provenance@v1
+        with:
+          subject-name: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+          subject-digest: ${{ steps.push.outputs.digest }}
+          push-to-registry: true
+

.github/workflows/pypi_release.yaml

@@ -0,0 +1,29 @@
+name: PyPI Release
+
+on:
+  release:
+    types: [published]
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/dbcan
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+      - run: python -m pip install --upgrade pip wheel twine build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/test.yaml

@@ -0,0 +1,84 @@
+name: Test
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+  schedule:
+    - cron: "0 5 1,15 * *"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0} # -e to fail on error
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-13]
+        python: ["3.7", "3.8", "3.9", "3.10", "3.11"]
+
+    name: ${{ matrix.name }} Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      # - name: Set up Python ${{ matrix.python }}
+      #   uses: actions/setup-python@v4
+      #   with:
+      #     python-version: ${{ matrix.python }}
+      #     cache: "pip"
+      #     cache-dependency-path: "**/pyproject.toml"
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          mamba-version: "*"
+          auto-update-conda: true
+          auto-activate-base: false
+          python-version: ${{ matrix.python }}
+          channels: conda-forge, bioconda, defaults
+          activate-environment: test_dbcan
+          environment-file: envs/test.yml
+
+      - name: export test_dbcan environment
+        run: mamba env export
+
+      # - name: Install test dependencies
+      #   run: |
+      #     python -m pip install --upgrade pip wheel
+      # - name: create run_dbcan environment
+      #   run: conda create -n run_dbcan python=${{ matrix.python }}
+      # - name: activate run_dbcan environment
+      #   run: conda activate run_dbcan
+
+      - name: Install dependencies
+        run: |
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
+
+      # - name: Add conda to PATH
+      #   run: |
+      #     echo ::add-path::$CONDA/bin
+
+      - name: Build dbCAN Database
+        run: |
+          dbcan_build --cpus 1 --db-dir db --clean
+          # conda install -y -c bioconda -c conda-forge hmmer diamond blast prodigal
+
+      - name: Test
+        env:
+          MPLBACKEND: agg
+          PLATFORM: ${{ matrix.os }}
+          DISPLAY: :42
+        run: |
+          coverage run -m pytest -v --color=yes

.github/workflows/testpypi_release.yaml

@@ -0,0 +1,32 @@
+name: Test PyPI Release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+# Use "trusted publishing", see https://docs.pypi.org/trusted-publishers/
+jobs:
+  release:
+    name: Publish pre-release Python distributions to TestPyPI
+    runs-on: ubuntu-latest
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/dbcan
+    permissions:
+      id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+      - run: python -m pip install --upgrade pip wheel twine build
+      - run: python -m build
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.gitignore

@@ -32,7 +32,6 @@ wheels/
 *.egg
 MANIFEST
 output*
-.vscode/
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
@@ -127,10 +126,12 @@ conda-recipe/meta.yaml
 
 Hotpep_bkp*
 
-#ignore example data
-EscheriaColiK12MG1655.*
-
 
 34*
 
-output*
+# IDE
+.idea/
+.vscode/
+
+# ignore version file
+**/_version.py

.pre-commit-config.yaml

@@ -41,6 +41,7 @@ repos:
       - id: trailing-whitespace
       - id: check-case-conflict
       - id: check-added-large-files
+        args: ["--maxkb=5000"]
       - id: check-toml
       - id: check-yaml
       - id: check-merge-conflict