Code Cleanup (#16)

* Improved inline and external documentation

* Attempt to make kernel density clearer

* Run precommit hooks

* Add more testing, including plot testing

* Some function refactoring

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.4.0
+current_version = 0.4.4
 tag = True
 commit = True
 

.cruft.json

@@ -1,23 +1,23 @@
 {
-  "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "28f47a97470826ca5000df24fd272e0d32d1c6fa",
-  "checkout": "v0.1.0",
-  "context": {
-    "cookiecutter": {
-      "project_name": "monkeybread",
-      "package_name": "monkeybread",
-      "project_description": "Tool for analyzing cell closeness in spatial transcriptomic data",
-      "author_full_name": "Immunitas Therapeutics",
-      "author_email": "[email protected]",
-      "github_user": "dillydally414",
-      "project_repo": "https://github.com/immunitastx/monkeybread",
-      "license": "MIT License",
-      "_copy_without_render": [
-        ".github/workflows/**.yaml",
-        "docs/_templates/autosummary/**.rst"
-      ],
-      "_template": "https://github.com/scverse/cookiecutter-scverse"
-    }
-  },
-  "directory": null
+    "template": "https://github.com/scverse/cookiecutter-scverse",
+    "commit": "28f47a97470826ca5000df24fd272e0d32d1c6fa",
+    "checkout": "v0.1.0",
+    "context": {
+        "cookiecutter": {
+            "project_name": "monkeybread",
+            "package_name": "monkeybread",
+            "project_description": "Tool for analyzing cell closeness in spatial transcriptomic data",
+            "author_full_name": "Immunitas Therapeutics",
+            "author_email": "[email protected]",
+            "github_user": "dillydally414",
+            "project_repo": "https://github.com/immunitastx/monkeybread",
+            "license": "MIT License",
+            "_copy_without_render": [
+                ".github/workflows/**.yaml",
+                "docs/_templates/autosummary/**.rst"
+            ],
+            "_template": "https://github.com/scverse/cookiecutter-scverse"
+        }
+    },
+    "directory": null
 }

.github/workflows/build.yaml

@@ -17,6 +17,8 @@ jobs:
                   python-version: "3.10"
             - name: Install build dependencies
               run: python -m pip install --upgrade pip wheel twine build
+            - name: Fix pkginfo version
+              run: pip install pkginfo==1.8.3
             - name: Build package
               run: python -m build
             - name: Check package

.github/workflows/test.yaml

@@ -55,6 +55,7 @@ jobs:
                   DISPLAY: :42
               run: |
                   pytest -v --cov --color=yes
+
 #            - name: Upload coverage
 #              env:
 #                  CODECOV_NAME: ${{ matrix.python }}-${{ matrix.os }}

.gitignore

@@ -77,3 +77,6 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# Test figures
+/tests/plot/figures/

CHANGELOG.md

@@ -8,6 +8,35 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## [0.4.4] - 2022-11-29
+
+### Added
+
+-   `mb.calc.neighborhood_profile` can take in a number of nearest neighbors to consider instead of radius
+
+### Changed
+
+-   `mb.plot.cell_contact_heatmap` sorts categories
+
+## [0.4.3] - 2022-11-28
+
+### Changed
+
+-   `mb.calc.shortest_distances` now returns a DataFrame for easier indexing
+-   `mb.plot.cell_transcript_proximity` uses predetermined colors if previously added by Scanpy
+
+## [0.4.2] - 2022-11-23
+
+### Fixed
+
+-   Fixed calculation in shortest distance statistical test
+
+## [0.4.1] - 2022-11-22
+
+### Added
+
+-   Basis customization to functions using coordinates
+
 ## [0.4.0] - 2022-11-21
 
 ### Added

DOCS_README.md

@@ -0,0 +1,57 @@
+# monkeybread
+
+[![Tests][badge-tests]][link-tests]
+[![Documentation][badge-docs]][link-docs]
+
+[badge-tests]: https://img.shields.io/github/workflow/status/immunitastx/monkeybread/Test/main
+[link-tests]: https://github.com/immunitastx/monkeybread/actions/workflows/test.yml
+[badge-docs]: https://img.shields.io/readthedocs/monkeybread
+
+Tool for analyzing cell closeness in spatial transcriptomic data. Developed at
+[Immunitas Therapeutics](https://www.immunitastx.com/).
+
+## Getting started
+
+Please refer to the [documentation][link-docs]. In particular, the
+
+-   [API documentation][link-api].
+
+## Installation
+
+You need to have Python 3.8 or newer installed on your system. If you don't have
+Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
+
+There are several alternative options to install monkeybread:
+
+<!--
+1) Install the latest release of `monkeybread` from `PyPI <https://pypi.org/project/monkeybread/>`_:
+
+```bash
+pip install monkeybread
+```
+-->
+
+1. Install the latest development version:
+
+```bash
+pip install git+https://github.com/immunitastx/monkeybread.git@main
+```
+
+## Release notes
+
+See the [changelog][changelog].
+
+## Contact
+
+For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
+If you found a bug, please use the [issue tracker][issue-tracker].
+
+## Citation
+
+> t.b.a
+
+[scverse-discourse]: https://discourse.scverse.org/
+[issue-tracker]: https://github.com/immunitastx/monkeybread/issues
+[changelog]: https://monkeybread.readthedocs.io/en/latest/changelog.html
+[link-docs]: https://monkeybread.readthedocs.io
+[link-api]: https://monkeybread.readthedocs.io/en/latest/api.html