try to switch to dev-env.yml file

.devcontainer.json

@@ -0,0 +1,41 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/ubuntu
+{
+	"name": "Ubuntu",
+	// Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+	"image": "mcr.microsoft.com/devcontainers/base:jammy",
+	"features": {
+		"ghcr.io/rocker-org/devcontainer-features/miniforge:1": {
+			"version": "latest",
+			"variant": "Mambaforge"
+		}
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	"postCreateCommand": "mamba env create -n happler -f dev-env.yml && conda run -n happler poetry install",
+
+	// Configure tool-specific properties.
+	"customizations": {
+		"vscode": {
+			"extensions": ["ms-python.python"],
+			"settings": {
+				"python.condaPath": "/opt/conda/condabin/conda",
+				"python.defaultInterpreterPath": "/opt/conda/envs/happler/bin/python",
+				"python.terminal.activateEnvironment": true,
+				"python.terminal.activateEnvInCurrentTerminal": true,
+				"python.venvFolders": ["/home/vscode/.cache/pypoetry/virtualenvs"],
+				"terminal.integrated.environmentChangesRelaunch": true,
+				"terminal.integrated.hideOnStartup": "always"
+			}
+		}
+	}
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	// "remoteUser": "root"
+}

.github/pull_request_template.md

@@ -0,0 +1,13 @@
+## Checklist
+
+* [ ] I've checked to ensure there aren't already other open [pull requests](../../../pulls) for the same update/change
+* [ ] I've prefixed the title of my PR according to [the conventional commits specification](https://www.conventionalcommits.org/). If your PR fixes a bug, please prefix the PR with `fix: `. Otherwise, if it introduces a new feature, please prefix it with `feat: `. If it introduces a breaking change, please add an exclamation before the colon, like `feat!: `. If the scope of the PR changes because of a revision to it, please update the PR title, since the title will be used in our CHANGELOG.
+* [ ] At the top of the PR, I've [listed any open issues that this PR will resolve](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue#linking-a-pull-request-to-an-issue-using-a-keyword). For example, "resolves #0" if this PR resolves issue #0
+- [ ] I've explained my changes in a manner that will make it possible for both users and maintainers of happler to understand them
+* [ ] I have followed the [contributing guidelines](https://happler.readthedocs.io/en/stable/project_info/contributing.html#how-to-fix-a-bug-or-implement-a-new-feature)
+* [ ] I have adhered to the [style guidelines](https://happler.readthedocs.io/en/stable/project_info/contributing.html#style)
+* [ ] I've added tests for any new functionality. Or, if this PR fixes a bug, I've added test(s) that replicate it
+* [ ] I've updated the relevant documentation and checked that the newly built documentation is formatted properly
+* [ ] All functions, modules, classes etc. still conform to [numpy docstring standards](https://numpydoc.readthedocs.io/en/latest/format.html)
+* [ ] (if applicable) I've updated the pyproject.toml file with any changes I've made to happler's dependencies, and I've run `poetry lock --no-update` to ensure the lock file stays up to date and that our dependencies are locked to their minimum versions
+* [ ] In the body of this PR, I've included a short address to the reviewer highlighting one or two items that might deserve their focus

.github/workflows/tests.yml

@@ -1,7 +1,6 @@
 name: Tests
 
-on:
-  - pull_request
+on: [pull_request, workflow_call]
 
 jobs:
   tests:
@@ -11,13 +10,16 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { python: "3.7", os: "ubuntu-latest", session: "lint" }
+          - { python: "3.8", os: "ubuntu-latest", session: "lint" }
           - { python: "3.7", os: "ubuntu-latest", session: "tests" }
           - { 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: "macos-latest", session: "tests" }
+          - { python: "3.11", os: "ubuntu-latest", session: "tests" }
+          - { python: "3.12", os: "ubuntu-latest", session: "tests" }
+          # - { python: "3.11", os: "windows-latest", session: "tests" }
+          - { python: "3.9", os: "macos-latest", session: "tests" }
+          - { python: "3.8", os: "ubuntu-latest", session: "size" }
 
     env:
       NOXSESSION: ${{ matrix.session }}
@@ -26,90 +28,75 @@ jobs:
 
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v3
+      - name: Setup Mambaforge
+        uses: conda-incubator/setup-miniconda@v3
         with:
-          python-version: ${{ matrix.python }}
+          activate-environment: happler
+          miniforge-variant: Mambaforge
+          auto-activate-base: false
+          miniforge-version: latest
+          use-mamba: true
 
-      - name: Upgrade pip
-        run: |
-          pip install --constraint=.github/workflows/constraints.txt pip
-          pip --version
-      - name: Upgrade pip in virtual environments
-        shell: python
-        run: |
-          import os
-          import pip
-          with open(os.environ["GITHUB_ENV"], mode="a") as io:
-              print(f"VIRTUALENV_PIP={pip.__version__}", file=io)
-      - name: Install Poetry
+      - 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@v3
+        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 happler -f dev-env.yml
+        if: steps.cache.outputs.cache-hit != 'true'
+
+      - name: Try to build happler
+        shell: bash -el {0}
         run: |
-          pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
-          poetry --version
-      - name: Install Nox
+          poetry build --no-ansi
+
+      - name: Check distribution size
+        if: matrix.session == 'size'
         run: |
-          pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox
-          pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry
-          nox --version
-      - name: Run Nox
+          du -csh dist/*
+          # 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 a "tool.poetry.exclude" section of our pyproject.toml
+          # https://python-poetry.org/docs/pyproject/#include-and-exclude
+          [ $(du -b dist | cut -f1) -lt 300000 ]
+
+      - name: Run tests with nox
+        if: matrix.session != 'size'
+        shell: bash -el {0}
         run: |
-          nox --python=${{ matrix.python }}
+          nox --verbose --python=${{ matrix.python }}
+
       - name: Upload coverage data
         if: always() && matrix.session == 'tests'
         uses: "actions/upload-artifact@v3"
         with:
           name: coverage-data
           path: ".coverage.*"
+
   large-files:
     name: File sizes
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
+
       - name: Check for large files
         uses: actionsdesk/[email protected]
         with:
           token: ${{ secrets.GITHUB_TOKEN }} # Optional
           filesizelimit: 500000b
           labelName: large-files
-
-  # coverage:
-  #   runs-on: ubuntu-latest
-  #   needs: tests
-  #   steps:
-  #     - name: Check out the repository
-  #       uses: actions/checkout@v3
-
-  #     - name: Set up Python
-  #       uses: actions/setup-python@v3
-  #       with:
-  #         python-version: "3.10"
-
-  #     - name: Upgrade pip
-  #       run: |
-  #         pip install --constraint=.github/workflows/constraints.txt pip
-  #         pip --version
-  #     - name: Install Poetry
-  #       run: |
-  #         pipx install --pip-args=--constraint=.github/workflows/constraints.txt poetry
-  #         poetry --version
-  #     - name: Install Nox
-  #       run: |
-  #         pipx install --pip-args=--constraint=.github/workflows/constraints.txt nox
-  #         pipx inject --pip-args=--constraint=.github/workflows/constraints.txt nox nox-poetry
-  #         nox --version
-  #     - name: Download coverage data
-  #       uses: actions/download-artifact@v3
-  #       with:
-  #         name: coverage-data
-
-  #     - name: Combine coverage data and display human readable report
-  #       run: |
-  #         nox --session=coverage
-  #     - name: Create coverage report
-  #       run: |
-  #         nox --session=coverage -- xml
-  #     - name: Upload coverage report
-  #       uses: codecov/[email protected]

.readthedocs.yaml

@@ -2,18 +2,26 @@
 # Read the Docs configuration file
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
 
-# Note: I used https://github.com/readthedocs/readthedocs.org/issues/4912#issuecomment-664002569 for inspiration
+# Note: I used https://docs.readthedocs.io/en/stable/build-customization.html#install-dependencies-with-poetry for inspiration
 
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.8"
+  jobs:
+    post_create_environment:
+      # Install poetry
+      # https://python-poetry.org/docs/#installing-manually
+      - pip install poetry
+      # Tell poetry to not use a virtual environment
+      - poetry config virtualenvs.create false
+    post_install:
+      # Install dependencies with 'docs' dependency group
+      # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
+      - poetry install --only main,docs
+
 sphinx:
   configuration: docs/conf.py
-
-python:
-  version: 3.7
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
-
+  fail_on_warning: true

dev-env.yml

@@ -0,0 +1,13 @@
+channels:
+  - conda-forge
+  - bioconda
+  - nodefaults
+dependencies:
+  - conda-forge::python=3.8 # the lowest version of python that we formally support
+  - conda-forge::pip==23.3.2
+  - conda-forge::poetry==1.7.1
+  - conda-forge::nox==2023.04.22
+  - conda-forge::poetry-plugin-export==1.6.0
+  - pip:
+    - nox-poetry==1.0.3
+    - poetry-conda==0.1.1