Advanced next into qa (#218)

* [pre-commit.ci] pre-commit autoupdate (#158)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.1 → v0.14.2](astral-sh/ruff-pre-commit@v0.14.1...v0.14.2)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* update refspec for test data

* [pre-commit.ci] pre-commit autoupdate (#160)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.2 → v0.14.4](astral-sh/ruff-pre-commit@v0.14.2...v0.14.4)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Bump prefix-dev/setup-pixi from 0.9.2 to 0.9.3 (#159)

Bumps [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi) from 0.9.2 to 0.9.3.
- [Release notes](https://github.com/prefix-dev/setup-pixi/releases)
- [Commits](prefix-dev/setup-pixi@v0.9.2...v0.9.3)

---
updated-dependencies:
- dependency-name: prefix-dev/setup-pixi
  dependency-version: 0.9.3
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump actions/checkout from 5 to 6 (#162)

Bumps [actions/checkout](https://github.com/actions/checkout) from 5 to 6.
- [Release notes](https://github.com/actions/checkout/releases)
- [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md)
- [Commits](actions/checkout@v5...v6)

---
updated-dependencies:
- dependency-name: actions/checkout
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#161)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.4 → v0.14.7](astral-sh/ruff-pre-commit@v0.14.4...v0.14.7)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#203)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.7 → v0.14.8](astral-sh/ruff-pre-commit@v0.14.7...v0.14.8)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* Bump peter-evans/create-pull-request from 7 to 8 (#211)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 7 to 8.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](peter-evans/create-pull-request@v7...v8)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-version: '8'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#212)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.8 → v0.14.9](astral-sh/ruff-pre-commit@v0.14.8...v0.14.9)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#214)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.9 → v0.14.10](astral-sh/ruff-pre-commit@v0.14.9...v0.14.10)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* [pre-commit.ci] pre-commit autoupdate (#216)

updates:
- [github.com/astral-sh/ruff-pre-commit: v0.14.10 → v0.14.11](astral-sh/ruff-pre-commit@v0.14.10...v0.14.11)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* docs: comprehensive documentation overhaul (#98) (#215)

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Author: 3 people

.github/workflows/package.yaml

@@ -14,8 +14,8 @@ jobs:
       # IMPORTANT: this permission is mandatory for trusted publishing
       id-token: write
     steps:
-      - uses: actions/checkout@v5
-      - uses: prefix-dev/setup-pixi@v0.9.2
+      - uses: actions/checkout@v6
+      - uses: prefix-dev/setup-pixi@v0.9.3
         with:
           pixi-version: v0.41.4
           manifest-path: pyproject.toml

.github/workflows/unittest.yaml

@@ -11,8 +11,8 @@ jobs:
   linux:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
-      - uses: prefix-dev/setup-pixi@v0.9.2
+      - uses: actions/checkout@v6
+      - uses: prefix-dev/setup-pixi@v0.9.3
         with:
           pixi-version: v0.41.4
           manifest-path: pyproject.toml

.github/workflows/update-lockfiles.yml

@@ -13,17 +13,17 @@ jobs:
   pixi-update:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
       - name: Set up pixi
-        uses: prefix-dev/setup-pixi@v0.9.2
+        uses: prefix-dev/setup-pixi@v0.9.3
         with:
           run-install: false
       - name: Update lockfiles
         run: |
           set -o pipefail
           pixi update --json | pixi exec pixi-diff-to-markdown >> diff.md
       - name: Create pull request
-        uses: peter-evans/create-pull-request@v7
+        uses: peter-evans/create-pull-request@v8
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Update pixi lockfile

.pre-commit-config.yaml

@@ -13,7 +13,7 @@ repos:
     - id: trailing-whitespace
       exclude: "(tests/data/.*|legacy/.*|src/pleiades/nuclear/isotopes/files/.*|src/pleiades/nuclear/isotope/files/.*|src/pleiades/nuclear/resonances/.*)"
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.14.1
+  rev: v0.14.11
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

.readthedocs.yaml

@@ -27,7 +27,5 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
-
-   # I WILL NEED TO INCLUDE THIS ONCE I HAVE MADE A PYTHON PACKAGE on PYPI.org
-   #- method: pip
-   #  path: .
+   - method: pip
+     path: .

docs/api/index.rst

@@ -0,0 +1,30 @@
+API Reference
+=============
+
+This section contains auto-generated API documentation from source docstrings.
+
+Core User API
+-------------
+
+The main user-facing modules for working with PLEIADES:
+
+.. toctree::
+   :maxdepth: 2
+
+   pleiades.sammy
+   pleiades.nuclear
+   pleiades.processing
+   pleiades.utils
+
+Supporting Modules
+------------------
+
+Additional modules and utilities:
+
+.. toctree::
+   :maxdepth: 2
+
+   pleiades.core
+   pleiades.experimental
+   pleiades.results
+   pleiades.post_install

docs/api/pleiades.core.constants.rst

@@ -0,0 +1,7 @@
+pleiades.core.constants module
+==============================
+
+.. automodule:: pleiades.core.constants
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/api/pleiades.core.rst

@@ -0,0 +1,15 @@
+pleiades.core package
+=====================
+
+.. automodule:: pleiades.core
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pleiades.core.constants

docs/api/pleiades.experimental.models.rst

@@ -0,0 +1,7 @@
+pleiades.experimental.models module
+===================================
+
+.. automodule:: pleiades.experimental.models
+   :members:
+   :show-inheritance:
+   :undoc-members:

docs/api/pleiades.experimental.rst

@@ -0,0 +1,15 @@
+pleiades.experimental package
+=============================
+
+.. automodule:: pleiades.experimental
+   :members:
+   :show-inheritance:
+   :undoc-members:
+
+Submodules
+----------
+
+.. toctree::
+   :maxdepth: 4
+
+   pleiades.experimental.models