MNT bump to v3.0.0

.github/ISSUE_TEMPLATE/bug-report.md

@@ -1,38 +1,54 @@
 ---
 name: Bug report
-about: Create a report to help us improve
-title: ''
-labels: ''
-assignees: eboileau
-
+about: Create a report to help us improve Rp-Bp
+title: ""
+labels: "T: bug"
+assignees: ""
 ---
 
-**Prerequisites**
-Please answer the following questions for yourself before submitting an issue.
+<!--
+Please make sure that the bug is not already fixed either in newer versions or the
+current development version.
+
+1. Update version if a newer release exists: `conda update rpbp` or
+2. Use the dev branch:
+   - create a conda environment and only install dependencies;
+   - clone this repository;
+   - run `pip install --no-deps -e .[test]`;
+   - make sure it works by running `python -m pytest`.
 
-- [ ] I am running the latest version, and specified versions of the dependencies 
-- [ ] I checked the documentation and found no answer
-- [ ] This issue has not already been filed
+If the bug persists, please make sure that it has not already been filed before
+opening a duplicate issue.
+-->
 
 **Description**
-A clear and concise description of what the issue is.
+
+<!-- A clear and concise description of what the bug is. -->
 
 **Expected behavior**
-A clear and concise description of what the expected behavior is.
+
+<!-- A clear and concise description of what the expected behavior is. -->
 
 **To Reproduce**
-Describe detailed steps to reproduce the issue:
+
+<!--
+Minimal steps to reproduce the bug:
+
 1. step 1
 2. step 2
 3. you get it...
+-->
 
 **Output**
-If relevant, paste the output of the steps above, including the commands themselves and traceback, etc.
+
+<!-- If relevant, paste the output of the steps above, including the commands themselves and traceback, etc. -->
 
 **Environment**
- - Pip version
- - Python version
- - Operating system
+
+- Version of the package
+- Conda/pip version and if relevant output of `conda list` or `pip freeze`
+- Operating system and Python version <!-- e.g. [Linux/Python 3.10.6] -->
 
 **Additional context**
-Add any other context about the problem here.
+
+<!-- Add any other context about the problem here. -->

.github/ISSUE_TEMPLATE/feature-request.md

@@ -0,0 +1,28 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: ""
+labels: "T: enhancement"
+assignees: ""
+---
+
+**Is your feature request related to a problem?**
+
+<!-- A clear and concise description of what the problem is.
+e.g. I would like to use the Rp-Bp output to do this, but [...] -->
+
+**Describe a possible solution**
+
+<!-- A clear and concise description of what you want to
+happen. -->
+
+**Did you consider alternative solutions?**
+
+<!-- A clear and concise description of any
+alternative solutions or features you've considered. Maybe a
+separate program/software, etc. can do that? -->
+
+**Additional context**
+
+<!-- Add any other context or screenshots about the feature request
+here. -->

.github/workflows/ci.yml

@@ -0,0 +1,59 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - master
+      - dev
+  pull_request:
+    branches:
+      - master
+      - dev
+
+jobs:
+  install-and-test:
+    runs-on: ${{matrix.os}}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Create rpbp conda environment
+        uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          channels: bioconda,conda-forge,defaults
+          channel-priority: true
+          auto-update-conda: true
+          auto-activate-base: false
+          activate-environment: rpbp
+          environment-file: environment.yml
+      - name: Display conda env info
+        run: |
+          conda info
+          conda list
+          conda config --show-sources
+          conda config --show
+          printenv | sort
+      - name: Install test requirements
+        run: pip install pytest pytest-cov pytest-depends
+      - name: Install rp-bp with --no-deps option
+        run: pip install . --no-deps --verbose
+      - name: Run tests
+        run: python -m pytest . --cov=rpbp --cov-report=xml -s -v
+      - name: Compile stan models (should already exist -> no-op)
+        run: compile-rpbp-models
+      - name: Compile stan models with --force
+        run: compile-rpbp-models --force
+      - name: Upload code coverage to codecov
+        uses: codecov/codecov-action@v3
+        with:
+          files: ./coverage.xml
+          name: ${{ matrix.os }}
+          fail_ci_if_error: true
+          verbose: true

.github/workflows/pypi.yml

@@ -0,0 +1,21 @@
+name: PyPI
+
+on:
+  push:
+    tags:
+      - "*.*.*"
+jobs:
+  pypi:
+    name: Upload to PyPI
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - run: pip install --upgrade build
+      - run: python -m build
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_token }}

.gitignore

@@ -1,6 +1,44 @@
-*checkpoint.ipynb
-*egg-info
-__pycache__
+# Byte-compiled, optimized, etc.
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# Sphinx documentation
+docs/_build/
+docs/build/
+docs/source/_build/
+doc/source/build/
+_readthedocs/
+
+# Local and other files
+/local/
+/data/
+
 *pkl
 *bbl
 *blg
@@ -10,22 +48,21 @@ __pycache__
 *vim
 *swp
 *orig
-
-scratch*ipynb
-
 *bak
 
-old
-src
-OpenBLAS
-data
+# Environments
+.env
+.venv
+env/
+venv/
+env.bak/
+venv.bak/
 
+# Example data
 c-elegans*
 
-docs/_build/
-docs/_static/
-docs/_templates/
-_build
-_static
-_templates
-
+# Stan models (compiled)
+src/rpbp/models/*
+!src/rpbp/models/**/
+src/rpbp/models/**/*/*
+!src/rpbp/models/**/*.stan

.pre-commit-config.yaml

@@ -0,0 +1,45 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: requirements-txt-fixer
+      - id: mixed-line-ending
+      - id: check-toml
+
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+      - id: black-jupyter
+
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.5.0
+    hooks:
+      - id: nbstripout
+
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: v2.7.1
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - [email protected]
+          - "prettier-plugin-toml"
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.17.1
+    hooks:
+      - id: check-github-workflows
+      - id: check-readthedocs
+
+  - repo: https://github.com/pycqa/flake8
+    rev: "5.0.4"
+    hooks:
+      - id: flake8
+        args:
+          - "--max-line-length=88"
+          - "--ignore=E203,E265,E266,E501,F401,W503,W605,E722,E731,E741,F841"
+ci:
+  autoupdate_schedule: quarterly

.readthedocs.yaml

@@ -1,6 +1,23 @@
-# .readthedocs.yml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+# https://docs.readthedocs.io/en/stable/config-file/v2.html
+
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.9"
+
+sphinx:
+  builder: html
+  configuration: docs/source/conf.py
+  fail_on_warning: false
+
+formats:
+  - pdf
 
 python:
-  version: 3.6
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs