Merge pull request #30 from gymrek-lab/citrus-package-setup

Initial package setup with poetry and tests

.github/workflows/tests.yml

@@ -0,0 +1,100 @@
+name: Tests
+
+on: [pull_request, workflow_call]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  tests:
+    name: ${{ matrix.session }} / ${{ matrix.python }} / ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - { python: "3.11", os: "ubuntu-latest", session: "tests" }
+          - { python: "3.12", os: "ubuntu-latest", session: "tests" }
+
+    env:
+      NOXSESSION: ${{ matrix.session }}
+      FORCE_COLOR: "1"
+      PRE_COMMIT_COLOR: "always"
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: citrus
+          miniforge-variant: Mambaforge
+          auto-activate-base: false
+          miniforge-version: latest
+          use-mamba: true
+
+      - name: Get Date
+        id: get-date
+        run: echo "today=$(/bin/date -u '+%Y%m%d')" >> $GITHUB_OUTPUT
+        shell: bash
+
+      - name: Cache Conda env
+        uses: actions/cache@v4
+        with:
+          path: ${{ env.CONDA }}/envs
+          key:
+            conda-${{ runner.os }}--${{ runner.arch }}--${{ steps.get-date.outputs.today }}-${{ hashFiles('dev-env.yml') }}-${{ env.CACHE_NUMBER }}
+        env:
+          # Increase this value to reset cache if dev-env.yml has not changed
+          CACHE_NUMBER: 0
+        id: cache
+
+      - name: Install dev environment
+        run:
+          mamba env update -n citrus -f dev-env.yml
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Try to build citrus
+        shell: bash -el {0}
+        run: |
+          poetry build --no-ansi
+
+      - name: Check distribution size
+        if: matrix.session == 'size'
+        run: |
+          du -csh dist/*
+          tar -ztvf dist/*.tar.gz
+          # check that the generated dist/ directory does not exceed 0.3 MB
+          # if this check fails, it's because you forgot to list large files in the "exclude" section of our pyproject.toml
+          # https://python-poetry.org/docs/pyproject/#include-and-exclude
+          [ $(du -b dist | cut -f1) -lt 300000 ]
+
+      - name: Check code coverage
+        if: matrix.session == 'coverage'
+        shell: bash -el {0}
+        run: |
+          export NOXSESSION=tests
+          # check that code coverage is not lower than specific percent
+          nox --verbose --python=${{ matrix.python }} -- --cov=. --cov-report=term-missing --cov-fail-under=0 # TODO update!!
+
+      - name: Run tests with nox
+        if: matrix.session == 'tests'
+        shell: bash -el {0}
+        run: |
+          nox --verbose --python=${{ matrix.python }}
+
+  large-files:
+    name: File sizes
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+
+      - name: Check for large files
+        uses: actionsdesk/[email protected]
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }} # Optional
+          filesizelimit: 500000b
+          labelName: large-files

README.md

@@ -10,13 +10,31 @@ CITRUS, the CIs and Trans inteRaction nUmerical Simulator, is a tool for simulat
 
 [Command Line Interface](doc/cli.md)
 
-
 ## Installation
 
+For plotting models, you will need to have [graphviz](https://graphviz.org/) installed.
+
+### With conda 
+
+**TODO - conda install instructions**
+
+### With pip 
+
+**TODO - pip install instructions**
+
 ### From source
 
+To install from source (only recommended for development), clone the CITRUS repository and checkout the branch you're interested in:
+
 ```bash
 git clone https://github.com/gymrek-lab/CITRUS.git
 cd CITRUS
-pip install .
 ```
+
+Now, create 1) a conda environment with our development tools and 2) a virtual environment with our dependencies and an editable install of CITRUS:
+
+```
+conda env create -n citrus -f dev-env.yml
+conda run -n citrus poetry install
+conda activate citrus
+```

citrus/__init__.py

@@ -0,0 +1,6 @@
+from importlib.metadata import version, PackageNotFoundError
+
+try:
+    __version__ = version(__name__)
+except PackageNotFoundError:
+    __version__ = "unknown"

citrus/tests/test_citrus.py

@@ -0,0 +1,5 @@
+import pytest
+
+# To check pytest framework is working
+def test_dummy():
+	assert True

dev-env.yml

@@ -0,0 +1,14 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - conda-forge::python=3.11 # the lowest version of python that we formally support
+  - conda-forge::pip==24.0
+  - conda-forge::poetry==1.8.3 # keep in sync with release.yml
+  - conda-forge::nox==2024.4.15
+  - conda-forge::poetry-plugin-export==1.8.0
+  - anaconda::graphviz==2.50.0
+  - pip:
+    - nox-poetry==1.0.3
+    - poetry-conda==0.1.1

example-files/linear_additive.json

@@ -0,0 +1,70 @@
+{
+	"input": [
+		{
+			"file": "example-files/example_gts_chr19.vcf.gz",
+			"file_format": "vcf",
+			"reference_genome": "GRCh37",
+			"force_bgz": true,
+			"input_nodes": [
+				{
+					"alias": "chr19_280540_G_A",
+					"type": "SNP",
+					"chr": "19",
+					"pos": 280540
+				},
+				{
+					"alias": "chr19_523746_C_T",
+					"type": "SNP",
+					"chr": "19",
+					"pos": [523746]
+				}
+			]
+		}
+	],
+	"simulation_steps": [
+		{
+			"type": "Constant",
+			"alias": "chr19_280540_G_A_beta",
+			"input_match_size": "chr19_280540_G_A",
+			"constant": 0.1
+		},
+		{
+			"type": "Constant",
+			"alias": "chr19_523746_C_T_beta",
+			"input_match_size": "chr19_523746_C_T",
+			"constant": 0.3
+		},		
+		{
+			"type": "Product",
+			"alias": "chr19_280540_G_A_effect",
+			"input_aliases": [
+				"chr19_280540_G_A_beta", "chr19_280540_G_A"
+			]
+		},
+		{
+			"type": "Product",
+			"alias": "chr19_523746_C_T_effect",
+			"input_aliases": [
+				"chr19_523746_C_T_beta", "chr19_523746_C_T"
+			]
+		},
+		{
+			"type": "Concatenate",
+			"alias": "effects_by_haplotype",
+			"input_aliases": [
+				"chr19_280540_G_A_effect",
+				"chr19_523746_C_T_effect"
+			]
+		},
+		{
+			"type": "AdditiveCombine",
+			"alias": "effects",
+			"input_alias": "effects_by_haplotype"
+		},
+		{
+			"type": "SumReduce",
+			"alias": "phenotype",
+			"input_alias": "effects"
+		}
+	]
+}

noxfile.py

@@ -0,0 +1,69 @@
+"""Nox sessions."""
+import os
+from pathlib import Path
+
+import nox
+from nox_poetry import Session
+from nox_poetry import session
+
+
+package = "citrus"
+python_versions = ["3.11", "3.12"]
+nox.needs_version = ">= 2022.11.21"
+nox.options.sessions = (
+    "tests",
+)
+
+
+cov_cli_args = [
+    "--cov=.",
+    "--cov-report=term-missing",
+]
+
+
+def install_handle_python(session):
+    """
+    handle incompatibilities between python and other packages
+    see https://github.com/cjolowicz/nox-poetry/issues/1116
+    """
+    # install the latest versions of all dependencies for py3.9+
+    # but install the locked versions for < py3.9 to ensure some stability in the CI and
+    # help us understand when we need to bump our version constraints
+    if session._session.python in ("3.9", "3.10", "3.11", "3.12"):
+        session._session.install(".")
+    else:
+        session.install(".")
+
+
+# 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(
+            "numpy",
+            "pytest",
+            "pytest-cov",
+            channel="conda-forge",
+        )
+        install_handle_python(session)
+        session.run(
+           "python", "-m", "pytest", *cov_cli_args, *session.posargs
+        )
+        session.run("./test/cmdline_tests.sh", external=True)
+else:
+
+    @session(python=python_versions)
+    def tests(session: Session) -> None:
+        """Run the test suite."""
+        session.install("pytest", "pytest-cov")
+        install_handle_python_numpy(session)
+        session.run(
+            "python", "-m", "pytest", *cov_cli_args, *session.posargs
+        )
+        session.run("./test/cmdline_tests.sh", external=True)