Merge pull request #348 from cytomining/release-v1.0.0

bump: version 0.2.0 → 1.0.0

.readthedocs.yml

@@ -14,7 +14,7 @@ build:
     post_install:
       # Install dependencies with 'docs' dependency group
       # https://python-poetry.org/docs/managing-dependencies/#dependency-groups
-      - poetry install --with docs
+      - poetry install --with dev,docs --all-extras
 
 sphinx:
   builder: html

CHANGELOG.md

@@ -0,0 +1,51 @@
+## v1.0.0 (2023-10-29)
+
+[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v1.0.0)
+
+### BREAKING CHANGE
+
+- functions now use expect None type as argument where they previously expected a "none" string
+- **drop_outliers**:: change default outlier threshold to 500
+- **variance_threshold** change variance_threshold default to 0.01
+
+### Feat
+
+- add parquet support for all i/o functions
+- **annotate**: add function to convert SQLite to pandas DataFrame and merge additional metadata
+- **build**: switch to poetry for dependency management and builds
+- **cells**: Enable custom image table name for SQLite queries in cells.py
+- **deepprofiler**: add single cell output and normalization
+- **dev**: standardized dev process and workflows (See [CONTRIBUTING.md](CONTRIBUTING.md)):
+  - add vscode devcontainer and codespaces config
+  - add conventional commit standards and commitizen cli
+  - add pre-commit hooks for black, prettier, actionlint
+- **docs**: Add detailed single-cell profiling [walkthrough](https://pycytominer.readthedocs.io/en/latest/walkthroughs/single_cell_usage.html)
+- **utils**: cell_locations script to append X,Y locations to LoadData
+
+### Fix
+
+- **annotate**: add informative merge suffixes to platemap and external_metadata
+- **annotate**: add check before dropping well columns
+- **build**: remove python 3.7 support
+- **correlation**: Use numpy to calculate pearson corr of non NaN matrices
+- **load_profiles**: now works with PurePath types
+
+## v0.2.0 (2022-06-17)
+
+[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v0.2.0)
+
+### Feat
+
+- **collate**: support CellProfiler analyses directly from CellProfiler output files
+
+## v0.1.5 (2022-06-17)
+
+[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v0.1.5)
+
+### Fix
+
+- **merge_single_cells** - improve memory performance
+
+## v0.1 (2022-02-08)
+
+[Detailed Release Notes](https://github.com/cytomining/pycytominer/releases/tag/v0.1)

CITATION.cff

@@ -67,6 +67,6 @@ authors:
     orcid: https://orcid.org/0000-0002-0503-9348
 title: "Reproducible processing of image-based profiling representations with Pycytominer"
 # This version is updated using `cz bump` command
-version: "0.2.0"
+version: "1.0.0"
 license: BSD 3-Clause License
 repository-code: "https://github.com/cytomining/pycytominer"

CONTRIBUTING.md

@@ -21,6 +21,7 @@ If you are stuck, please feel free to ask any questions or ask for help.
 - [Documentation](#documentation)
 - [Poetry](#poetry)
 - [Dev environments](#dev-environments)
+- [Releases](#releases)
 
 [Style guides](#style-guides)
 
@@ -168,6 +169,24 @@ cd pycytominer
 bash .devcontainer/postCreateCommand.sh
 ```
 
+### Releases
+
+Project maintainers are responsible for releasing new versions of pycytominer.
+Creating a new release includes the following steps:
+
+1. Create a new branch from `main` for the release (e.g. `release-v1.0.0`)
+2. Run the command `cz bump --files-only` to update the version number in `CITATION.cff` and `pyproject.toml:tool.commitizen`.
+3. Review the changes to CHANGELOG.md and edit as needed.
+4. Review the [commit history](https://github.com/cytomining/pycytominer/compare) from the last release and add documentation for changes that weren't auto-included because they didn't follow the conventional-commit standard.
+5. `git add` all changes and run `cz bump` to create the release commit.
+6. Create a pull request for the release branch into `main`.
+7. Request a review from another maintainer.
+8. Once the pull request is approved, merge it into `main`.
+9. Create a new release on GitHub using the [release draft](https://github.com/cytomining/pycytominer/releases/new) feature.
+10. Publish the release.
+11. The release will be automatically published to [PyPI](https://pypi.org/project/pycytominer/) via Github Actions.
+12. Manually create the release at [conda-forge](https://anaconda.org/conda-forge/pycytominer).
+
 ## Style guides
 
 Please follow all style guides to the best of your abilities.

README.md

@@ -2,7 +2,7 @@
 
 # Data processing for image-based profiling
 
-[![Build Status](https://travis-ci.org/cytomining/pycytominer.svg?branch=main)](https://travis-ci.org/cytomining/pycytominer)
+[![Build Status](https://github.com/cytomining/pycytominer/actions/workflows/integration-test.yml/badge.svg?branch=main)](https://github.com/cytomining/pycytominer/actions/workflows/integration-test.yml?query=branch%3Amain)
 [![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/main/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=main)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 [![RTD](https://readthedocs.org/projects/pycytominer/badge/?version=latest&style=flat)](https://pycytominer.readthedocs.io/)

docs/conf.py

@@ -13,6 +13,7 @@
 import os
 import sys
 import pathlib
+import yaml
 from datetime import date
 
 sys.path.insert(0, os.path.abspath(".."))
@@ -27,8 +28,9 @@
     date=date.today().year, author=author
 )
 
-# The full version, including alpha/beta/rc tags
-version = pycytominer.__about__.__version__
+# The version from CITATION.cff is used to set the version of the package
+cff_path = pathlib.Path("..") / "CITATION.cff"
+version = yaml.safe_load(cff_path.read_text())["version"]
 release = version
 
 # -- General configuration ---------------------------------------------------

pyproject.toml

@@ -96,7 +96,7 @@ files = ["pycytominer/__about__.py"]
 
 [tool.commitizen]
 # This version is used for changelog tracking and is updated using `cz bump`
-version = "0.2.0"
+version = "1.0.0"
 name = "cz_conventional_commits"
 tag_format = "v$version"
 version_scheme = "pep440"