feat: github actions for publishing (#141)

.github/workflows/conventional-prs.yml

@@ -0,0 +1,22 @@
+name: Title
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+permissions:
+  contents: read
+
+jobs:
+  title-format:
+    permissions:
+      pull-requests: read  # for amannn/action-semantic-pull-request to analyze PRs
+      statuses: write  # for amannn/action-semantic-pull-request to mark status of analyzed PR
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,67 @@
+name: Release
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: python
+          package-name: haptools
+
+      - uses: actions/checkout@v3
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          fetch-depth: 2
+
+      - name: Set up Python
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: '3.7'
+
+      - name: Upgrade pip
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          pip install --constraint=.github/workflows/constraints.txt pip
+          pip --version
+
+      - name: Install Poetry
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          pip install --constraint=.github/workflows/constraints.txt poetry
+          poetry --version
+
+      - name: Bump version for developmental release
+        if: ${{ steps.release.outputs.release_created }}
+        env:
+          version: ${{ steps.release.outputs.tag_name }}
+        run: |
+          poetry version $version
+
+      - name: Build package
+        if: ${{ steps.release.outputs.release_created }}
+        run: |
+          poetry build --ansi
+
+      - name: Publish package on TestPyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: {{ "${{ secrets.TEST_PYPI_TOKEN }}" }}
+          repository_url: https://test.pypi.org/legacy/
+
+      - name: Publish package on PyPI
+        if: ${{ steps.release.outputs.release_created }}
+        uses: pypa/[email protected]
+        with:
+          user: __token__
+          password: {{ "${{ secrets.PYPI_TOKEN }}" }}

.github/workflows/tests.yml

@@ -1,13 +1,12 @@
 name: Tests
 
 on:
-  - push
   - pull_request
 
 jobs:
   tests:
-    name: ${{"{{"}} matrix.session {{"}}"}} ${{"{{"}} matrix.python {{"}}"}} / ${{"{{"}} matrix.os {{"}}"}}
-    runs-on: ${{"{{"}} matrix.os {{"}}"}}
+    name: ${{ matrix.session }} ${{ matrix.python }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
@@ -17,22 +16,22 @@ jobs:
           - { python: "3.8", os: "ubuntu-latest", session: "tests" }
           - { python: "3.9", os: "ubuntu-latest", session: "tests" }
           - { python: "3.10", os: "ubuntu-latest", session: "tests" }
-          - { python: "3.10", os: "windows-latest", session: "tests" }
+          # - { python: "3.10", os: "windows-latest", session: "tests" }
           - { python: "3.10", os: "macos-latest", session: "tests" }
 
     env:
-      NOXSESSION: ${{"{{"}} matrix.session {{"}}"}}
+      NOXSESSION: ${{ matrix.session }}
       FORCE_COLOR: "1"
       PRE_COMMIT_COLOR: "always"
 
     steps:
       - name: Check out the repository
         uses: actions/checkout@v3
 
-      - name: Set up Python ${{"{{"}} matrix.python {{"}}"}}
+      - name: Set up Python ${{ matrix.python }}
         uses: actions/setup-python@v3
         with:
-          python-version: ${{"{{"}} matrix.python {{"}}"}}
+          python-version: ${{ matrix.python }}
 
       - name: Upgrade pip
         run: |
@@ -56,7 +55,7 @@ jobs:
           nox --version
       - name: Run Nox
         run: |
-          nox --python=${{"{{"}} matrix.python {{"}}"}}
+          nox --python=${{ matrix.python }}
       - name: Upload coverage data
         if: always() && matrix.session == 'tests'
         uses: "actions/upload-artifact@v3"
@@ -101,4 +100,4 @@ jobs:
   #       run: |
   #         nox --session=coverage -- xml
   #     - name: Upload coverage report
-  #       uses: codecov/[email protected]
+  #       uses: codecov/[email protected]

docs/commands/simphenotype.rst

@@ -82,14 +82,21 @@ By default, all of the haplotypes in the ``.hap`` file will be encoded as causal
    haptools transform tests/data/example.vcf.gz tests/data/simphenotype.hap | \
    haptools simphenotype --id 'chr21.q.3365*1' /dev/stdin tests/data/simphenotype.hap
 
-To simulate ancestry-specific effects from a genotypes file with population labels, use the ``--ancestry`` switch when running ``transform``:
+To simulate ancestry-specific effects from a genotypes file with population labels, use the ``--ancestry`` switch when running ``transform``.
 
 .. code-block:: bash
 
    haptools transform --ancestry tests/data/simple-ancestry.vcf tests/data/simple.hap | \
    haptools simphenotype --id H1 /dev/stdin tests/data/simple.hap
 
-Simulate two replicates of a case/control trait that occurs in 60% of your samples with a heritability of 0.8. Encode all of the haplotypes in ``tests/data/example.hap.gz`` as independent causal variables.
+If speed is important, it's generally faster to use PGEN files than VCFs.
+
+.. code-block:: bash
+
+   haptools transform --output simple-haps.pgen tests/data/simple.pgen tests/data/simple.hap
+   haptools simphenotype --id H1 simple-haps.pgen tests/data/simple.hap
+
+Let's simulate two replicates of a case/control trait that occurs in 60% of samples with a heritability of 0.8. We'll encode only two of the haplotypes in ``tests/data/simphenotype.hap`` as independent causal variables.
 
 .. code-block:: bash
 
@@ -98,6 +105,8 @@ Simulate two replicates of a case/control trait that occurs in 60% of your sampl
    --replications 2 \
    --heritability 0.8 \
    --prevalence 0.6 \
+   --id 'chr21.q.3365*10' \
+   --id 'chr21.q.3365*11' \
    --output simulated.pheno \
    /dev/stdin tests/data/simphenotype.hap
 

docs/formats/genotypes.rst

@@ -18,9 +18,9 @@ Genotype files must be specified as VCF or BCF files. They can be bgzip-compress
 PLINK2 PGEN
 -----------
 
-There is also experimental support for `PLINK2 PGEN <https://github.com/chrchang/plink-ng/blob/master/pgen_spec/pgen_spec.pdf>`_ files in some commands. These files can be loaded much more quickly than VCFs, so we highly recommend using them if you're working with large datasets. See the documentation for the :class:`GenotypesPLINK` class in :ref:`the API docs <api-data-genotypesplink>` for more information.
+There is also experimental support for `PLINK2 PGEN <https://github.com/chrchang/plink-ng/blob/master/pgen_spec/pgen_spec.pdf>`_ files in some commands. These files can be loaded and created much more quickly than VCFs, so we highly recommend using them if you're working with large datasets. See the documentation for the :class:`GenotypesPLINK` class in :ref:`the API docs <api-data-genotypesplink>` for more information.
 
-If you run out memory when using PGEN files, consider reading variants from the file in chunks via the ``--chunk-size`` parameter.
+If you run out memory when using PGEN files, consider reading/writing variants from the file in chunks via the ``--chunk-size`` parameter.
 
 .. note::
 	PLINK2 support depends on the ``Pgenlib`` python library. This can be installed automatically with ``haptools`` if you specify the "files" extra requirements during installation.

docs/project_info/contributing.rst

@@ -96,29 +96,29 @@ For example, to add a pypi dependency to our list and install it, just run
 -----------
 Code Checks
 -----------
-Before creating your pull request, please run our code checks through ``nox``.
-
-.. code-block:: bash
-
-    nox
-
-You can also execute each of our code checks individually.
+Before creating your pull request, please run each of our code checks.
 
 1. Format the code correctly
 
     .. code-block:: bash
 
-        nox --session=lint
+        black .
 
 2. If you made changes to the docs, check that they appear correctly.
 
     .. code-block:: bash
 
-        nox --session=docs
-        open docs/_build/index.html
+        sphinx-build docs docs/_build
+        open docs/_build/html/index.html
 
 3. Run all of the tests
 
+    .. code-block:: bash
+
+        pytest tests/
+
+    You can also build the package and run the tests from the built version using ``nox``. This will fully simulate installing the package from PyPI.
+
     .. code-block:: bash
 
         nox --session=tests

noxfile.py

@@ -19,14 +19,7 @@
 )
 
 
-# detect whether mamba is installed
-conda_cmd = "conda"
-if (Path(os.getenv("CONDA_EXE")).parent / "mamba").exists():
-    conda_cmd = "mamba"
-conda_args = ["-c", "conda-forge"]
-
-
-@session(python=False)
+@session(python=python_versions[0])
 def docs(session: Session) -> None:
     """Build the documentation."""
     args = session.posargs or ["docs", "docs/_build"]
@@ -40,30 +33,58 @@ def docs(session: Session) -> None:
     session.run("sphinx-build", *args)
 
 
-@session(python=False)
+@session(python=python_versions[0])
 def lint(session: Session) -> None:
     """Lint our code."""
+    session.install("black")
     session.run("black", "--check", ".")
 
 
-@session(venv_backend=conda_cmd, venv_params=conda_args, python=python_versions)
-def tests(session: Session) -> None:
-    """Run the test suite."""
-    session.conda_install(
-        "coverage[toml]", "pytest", "numpy>=1.20.0", channel="conda-forge"
-    )
-    # TODO: change this to ".[files]" once plink-ng Alpha 3.8 is released
-    # https://github.com/chrchang/plink-ng/releases
-    session.install(".")
-
-    try:
-        session.run("coverage", "run", "--parallel", "-m", "pytest", *session.posargs)
-    finally:
-        if session.interactive:
-            session.notify("coverage", posargs=[])
-
-
-@session(python=False)
+# detect whether conda/mamba is installed
+if os.getenv("CONDA_EXE"):
+    conda_cmd = "conda"
+    if (Path(os.getenv("CONDA_EXE")).parent / "mamba").exists():
+        conda_cmd = "mamba"
+    conda_args = ["-c", "conda-forge"]
+
+    @session(venv_backend=conda_cmd, venv_params=conda_args, python=python_versions)
+    def tests(session: Session) -> None:
+        """Run the test suite."""
+        session.conda_install(
+            "coverage[toml]", "pytest", "numpy>=1.20.0", channel="conda-forge"
+        )
+        # TODO: change this to ".[files]" once plink-ng Alpha 3.8 is released
+        # https://github.com/chrchang/plink-ng/releases
+        session.install(".")
+
+        try:
+            session.run(
+                "coverage", "run", "--parallel", "-m", "pytest", *session.posargs
+            )
+        finally:
+            if session.interactive:
+                session.notify("coverage", posargs=[])
+
+else:
+
+    @session(python=python_versions)
+    def tests(session: Session) -> None:
+        """Run the test suite."""
+        session.install("coverage[toml]", "pytest")
+        # TODO: change this to ".[files]" once plink-ng Alpha 3.8 is released
+        # https://github.com/chrchang/plink-ng/releases
+        session.install(".")
+
+        try:
+            session.run(
+                "coverage", "run", "--parallel", "-m", "pytest", *session.posargs
+            )
+        finally:
+            if session.interactive:
+                session.notify("coverage", posargs=[])
+
+
+@session(python=python_versions[0])
 def coverage(session: Session) -> None:
     """Produce the coverage report."""
     args = session.posargs or ["report"]