Dev (#16)

* update changelog with unreleased changes

* use automated Zenodo releases instead of drafts

* update instructions for adding authors

* only build src/ folder

* update changelog

Author: mdtanker

.github/ISSUE_TEMPLATE/release_checklist.md

@@ -7,7 +7,6 @@ assignees: ''
 
 ---
 
-**Zenodo DOI:**
 
 <!-- Optional -->
 **Target date:** YYYY/MM/DD
@@ -16,24 +15,11 @@ assignees: ''
 
 - [ ] Check all the dependency changes since the last release are  reflected in `environment.yml`
 
-## Draft a Zenodo archive (to be done by a manager on Zenodo)
-
-- [ ] Go to the Zenodo entry for this project (find the link to the latest Zenodo release on the `README.md` file)
-- [ ] Create a "New version" of it.
-- [ ] Get a new DOI for the new release
-- [ ] Copy and paste the reserved DOI to this issue
-- [ ] Update release date
-- [ ] Update version number in Title (make sure there is a leading `v`, like `v1.5.7`)
-- [ ] Update version number (use a leading `v` as well)
-- [ ] Add as authors any new contributors who have added themselves to `AUTHORS.md` in the same order
-- [ ] Ensure that the first author is "samplepackagename Developers" and others are listed alphabetically by last name
-- [ ] Save the release draft
 
 ## Update the changelog
 
 - [ ] Generate a list of commits between the last release tag and now: `git log HEAD...v1.2.3 > changes.md`
 - [ ] Use this to summarize the major changes to the code and add short descriptions to `CHANGELOG.md` (not `docs/changelog.md`!).
-- [ ] Add the release date and Zenodo DOI badge to the top
 - [ ] Add contributors to the list
 - [ ] Open a PR to update the changelog
 - [ ] Merge the PR
@@ -44,14 +30,9 @@ After the changelog PR is merged:
 
 - [ ] Draft a new release on GitHub
 - [ ] The tag and release name should be a version number (following Semantic Versioning) with a leading `v` (`v1.5.7`)
-- [ ] Fill the release description with a Markdown version of the latest changelog entry (including the DOI badge)
+- [ ] Fill the release description with a Markdown version of the latest changelog entry
 - [ ] Publish the release
 
-## Publish to Zenodo
-
-- [ ] Upload the zip archive from the GitHub release to Zenodo
-- [ ] Double check all information (date, authors, version)
-- [ ] Publish the new version on Zenodo
 
 ## Conda-forge package
 

.github/config.yml

@@ -26,3 +26,4 @@ firstPRMergeComment: >
 
    We hope that this was a good experience for you. Let us know if there is any way that the contributing process could be improved.
 
+   Please add yourself as an author to both of the following files in a new PR: AUTHORS.md and .zenodo.json.

.gitignore

@@ -144,10 +144,12 @@ dmypy.json
 # Cython debug symbols
 cython_debug/
 
+# git changes
+changes.md
+
 # setuptools_scm
 src/*/_version.py
 
-
 # ruff
 .ruff_cache/
 

.zenodo.json

@@ -0,0 +1,11 @@
+{
+  "title": "samplepackagename: short description",
+  "description": "<p><strong>samplepackagename</strong> is a Python package ...</p><p><strong>Documentation</strong>: <a href=\"https://organizationname.github.io/samplepackagename/\">https://organizationname.github.io/samplepackagename/</a></p><p><strong>Source code</strong>: <a href=\"https://github.com/organizationname/samplepackagename\">https://github.com/organizationname/samplepackagename</a></p>",
+  "creators": [
+    {
+      "orcid": "your ORCID",
+      "affiliation": "Institute, Country",
+      "name": "Lastname, Firstname"
+    }
+  ]
+}

AUTHORS.md

@@ -1,6 +1,6 @@
-# Project Authors
+# samplepackagename Authors
 
 The following people have made contributions to the project (in alphabetical
 order by last name) and are considered "The samplepackagename Developers":
 
-* [name](https://github.com/<username>) - Institute, Country (ORCID: [<your ORDIC>](https://www.orcid.org/<your ORDIC>))
+* [Firstname, Lastname](https://github.com/<username>) - Institute, Country (ORCID: [<your ORCID>](https://www.orcid.org/<your ORCID>))

CHANGELOG.md

@@ -7,42 +7,57 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+### 🚀 Added
+- preview the docs in each PR with new GitHub Action
+- include a `.zenodo.json` file to set metadata for each Zenodo release
+
 ### ✏️ Changed
-* replace pre-commit GitHub action with pre-commit.ci
-* Switched website hosting from ReadTheDocs to GitHug Pages
-* Dropped support for Python 3.9, following the recommendation from [SPEC 0000](https://scientific-python.org/specs/spec-0000/)
+- replace pre-commit GitHub action with pre-commit.ci
+- Switched website hosting from ReadTheDocs to GitHug Pages
+- codespell now tries to ignore notebook outputs
+- improved the contribution guide
+- improved instructions for using this template
+- updated PyLint and MyPy ignored rules
+- removed forced-configuration of logging
+- use automated release of Zenodo from GitHub integration instead of manually drafting release
+- only build and distribute the `src/` directory when packaging
+
+### ❌ Removed
+- Dropped support for Python 3.9, following the recommendation from [SPEC 0000](https://scientific-python.org/specs/spec-0000/)
+
 <!--
 Below is an example for a release
 
-## 0.0.1
+## v0.0.1
 Released on 2025-06-04
-DOI: https://zenodo.org/records/148521
 Contributors:
-    * author1
-    * author2
+- author1
+- author2
 
 ### 🚀 Added
-
 - function `function2` for calculating something important.
 
 ### ✏️ Changed
-
 - Changed the lower bounds on the pandas dependency from v1.5 to v1.2.
 
 ### ⚠️ Deprecated
-
 - marked `function1` as deprecated, used the new `function2` instead.
 
 ### ❌ Removed
-
 - removed the previously deprecated `function0`.
 
 ### 🐛 Fixed
-
 - fixed a bug in `function1` which cause some error.
 
 ### 🛡️ Security
-
 - removed a password from the code.
 
 -->
+
+
+## v0.0.1
+Released on 2025-07-11
+Contributors:
+- Matt Tankersley
+
+Initial Release of Python_Package_Template!

CONTRIBUTING.md

@@ -53,6 +53,8 @@ contributions.
   - [Push your changes](#push-your-changes)
   - [Open a PR](#open-a-pr)
   - [Code review](#code-review)
+  - [Sync your fork and local](#sync-your-fork-and-local)
+  - [Add yourself as an author](#add-yourself-as-an-author)
 * [Publish a new release](#publish-a-new-release)
 * [Update the Dependencies](#update-the-dependencies)
 
@@ -373,6 +375,10 @@ git push origin main
 ```
 Now both your forked (upstream) and local repositories are sync with the upstream repository where the PR was merged.
 
+### Add yourself as an author
+
+Once you have merged your PR, open a new PR with your details added to the files `AUTHORS.md` and `.zenodo.json`. With each new release, Zenodo will add you as an author to package.
+
 ## Publish a new release
 
 This will almost always be done by the developers, but as a guide for them, here are instructions on how to release a new version of the package.

README.md

@@ -36,8 +36,8 @@ Steps:
         - your name can be "Maintainers of <samplepackagename>" if there are multiple people.
     - replace all instances of `organizationname` with your GitHub organization (or personal) account name, whichever is going to host the repository.
     - update `pyproject.yml` with a description (1 sentence) and keywords ()
-    - add a description of your project here in the README, as well as in `docs/index.md`.
-    - add your info to `AUTHORS.md`
+    - add a description of your project here in the README, in `docs/index.md`, and in `.zenodo.json`.
+    - add your info to `AUTHORS.md` and `.zenodo.json`
     - at this point, it might be good to make your initial commit to your repository with the following git commands:
         ```bash
         git checkout -b new-branch
@@ -151,6 +151,9 @@ Steps:
     - for every push to `main` (from a PR), the site will be updated
 14) Finalize
     - remove all the above instructions and raise any issues in this template's repository if you have any suggestion or found any errors in this template!
+    - replace all instances of "zenodo_DOI" in this repository with your new Zenodo DOI.
+        - if your Zenodo link is https://doi.org/10.5281/zenodo.15863068,, your DOI is just 15863068
+        - make sure to use the DOI from the `Cite all versions?` portion of your Zenodo page.
     - if you want, please submit a PR to this repository to add your package to this list at the top of this README to showcase it!
 
 # samplepackagename
@@ -162,6 +165,7 @@ Short description of your package.
 [![PyPI version][pypi-version]][pypi-link]
 [![Conda-Forge][conda-badge]][conda-link]
 [![PyPI platforms][pypi-platforms]][pypi-link]
+[![Zenodo][zenodo-badge]][zenodo-link]
 
 [![GitHub Discussion][github-discussions-badge]][github-discussions-link]
 
@@ -179,7 +183,8 @@ Short description of your package.
 [pypi-version]:             https://img.shields.io/pypi/v/samplepackagename
 [website-badge]:            https://github.com/organizationname/samplepackagename/actions/workflows/pages/pages-build-deployment/badge.svg
 [website-link]:             https://organizationname.github.io/samplepackagename/
-
+[zenodo-badge]:            https://zenodo.org/badge/DOI/10.5281/zenodo.zenodo_DOI.svg
+[zenodo-link]:             https://doi.org/10.5281/zenodo.zenodo_DOI
 <!-- prettier-ignore-end -->
 
 <!-- SPHINX-END-badges -->

docs/citing.md

@@ -4,4 +4,4 @@ This is research software made by scientists. Citations help us justify the effo
 
 If you used `samplepackagename` in your research, please consider citing our software.
 
-If you would like to cite the specific version you used, which can improve reproducibility and let users know the state of the software at the time of your analysis, please use the version-specific citation and DOI (available from [Zenodo](https://doi.org/10.5281/zenodo.15863068)).
+If you would like to cite the specific version you used, which can improve reproducibility and let users know the state of the software at the time of your analysis, please use the version-specific citation and DOI (available from [Zenodo](https://doi.org/10.5281/zenodo.zenodo_DOI)).

pyproject.toml

@@ -72,6 +72,8 @@ build.hooks.vcs.version-file = "src/samplepackagename/_version.py"
 dependencies = []
 scripts.test = "pytest {args}"
 
+[tool.hatch.build.targets.sdist]
+only-include = ["src"]
 
 [tool.pytest.ini_options]
 minversion = "6.0"