CIERA-Transients · KerryPaterson · Mar 10, 2026 · Sep 2, 2025 · Sep 2, 2025 · Sep 3, 2025
diff --git a/.coverage b/.coverage
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -29,18 +29,18 @@ jobs:
       shell: bash -l {0} # Use login shell for conda commands
       run: |
         conda env create -f environment.yml
-        conda activate potpyri_test
+        conda activate potpyri
 
     - name: Install the Package and Remaining Dependencies
       shell: bash -l {0}
       run: |
-          conda activate potpyri_test
+          conda activate potpyri
           python -m pip install --upgrade pip setuptools wheel
           pip install .
 
     - name: Run tests
       shell: bash -l {0}
       run: |
-          conda activate potpyri_test
+          conda activate potpyri
           pip install .[test]
-          pytest
+          pytest -m "not integration"
diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
@@ -34,6 +34,7 @@ jobs:
         cd docs
         make html
     - name: Deploy to GitHub Pages
+      if: github.event_name == 'push' && github.ref == 'refs/heads/main'
       uses: peaceiris/actions-gh-pages@v4
       with:
         publish_branch: gh-pages

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -0,0 +1,26 @@
+# Contributing to POTPyRI
+
+Thank you for your interest in contributing to POTPyRI. We welcome issues, suggestions, and pull requests.
+
+## Reporting issues
+
+If you encounter a bug, have a question about usage, or have a feature request:
+
+- **GitHub Issues:** Open an issue at [github.com/CIERA-Transients/POTPyRI/issues](https://github.com/CIERA-Transients/POTPyRI/issues). Please include a clear description, steps to reproduce (for bugs), and your environment (Python version, instrument, OS) where relevant.
+- **Email:** You can also contact the developers at `ckilpatrick@northwestern.edu` for matters you prefer not to discuss in the issue tracker.
+
+## Contributing code or documentation
+
+1. **Fork the repository** and create a branch (often from `dev` for ongoing development; the default branch may be `main`).
+2. **Make your changes** and add or update tests if applicable. Run the test suite with `pytest tests` (use `pytest tests -m "not integration"` for offline runs without fixture downloads).
+3. **Open a pull request** against the main repository (or against `dev` when that branch is used for integration). Describe your changes clearly and reference any related issues.
+4. **Code style:** Follow the existing style in the codebase. The project uses standard Python packaging and type hints where appropriate.
+
+Instrument-specific changes (e.g. new instruments or header/sorting logic) should include a brief justification and, if possible, a note in the PR description on how the change was tested.
+
+## Support
+
+- For **usage questions, bugs, or feature requests,** please open a [GitHub issue](https://github.com/CIERA-Transients/POTPyRI/issues).
+- For **other inquiries** (e.g. collaboration, adding an instrument), you can contact the developers at `ckilpatrick@northwestern.edu`.
+
+We aim to respond to issues and pull requests in a timely manner; please allow at least a week for non-urgent responses.
diff --git a/README.md b/README.md
diff --git a/docs/DEPLOY.md b/docs/DEPLOY.md
@@ -0,0 +1,37 @@
+# Deploying documentation to https://ciera-transients.github.io/POTPyRI/
+
+The docs are built with Sphinx and deployed to GitHub Pages via the `gh-pages` branch. The URL is a **project site**: `https://<org>.github.io/<repo>/` → `https://ciera-transients.github.io/POTPyRI/`.
+
+## One-time setup (repo maintainers)
+
+1. **Enable GitHub Pages**
+   - On GitHub: **Settings** → **Pages** (left sidebar).
+   - Under **Build and deployment**:
+     - **Source**: Deploy from a branch.
+     - **Branch**: choose `gh-pages`, folder **/ (root)**.
+     - Save.
+
+2. **First deployment**
+   - The workflow [`.github/workflows/documentation.yml`](../.github/workflows/documentation.yml) runs on every **push to `main`**.
+   - It builds the docs (`pip install .[docs]`, `cd docs && make html`) and pushes `docs/build/html/` to the `gh-pages` branch.
+   - After the first successful run, the site is available at https://ciera-transients.github.io/POTPyRI/ (can take a few minutes).
+
+3. **Pull requests**
+   - The same workflow runs on pull requests targeting `main`, but the **Deploy** step is skipped (deploy only runs on push to `main`). So PRs validate that the docs build without updating the live site.
+
+## Local build
+
+To build and view the docs locally:
+
+```bash
+pip install .[docs]
+cd docs && make html
+open build/html/index.html   # or open build/html/index.html on Linux
+```
+
+## Configuration
+
+- **Sphinx config**: `docs/source/conf.py` (e.g. `html_baseurl`, theme, extensions).
+- **Base URL**: `html_baseurl = 'https://CIERA-Transients.github.io/POTPyRI/'` is already set so links and assets resolve correctly on GitHub Pages.
+
+If the site returns 404 after enabling Pages, wait a few minutes and ensure the `gh-pages` branch exists and has content (run the workflow once by pushing to `main`).
diff --git a/docs/source/api/generated/potpyri.instruments.BINOSPEC.rst b/docs/source/api/generated/potpyri.instruments.BINOSPEC.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.BINOSPEC
+============================
+
+.. automodule:: potpyri.instruments.BINOSPEC
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      BINOSPEC
+
diff --git a/docs/source/api/generated/potpyri.instruments.DEIMOS.rst b/docs/source/api/generated/potpyri.instruments.DEIMOS.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.DEIMOS
+==========================
+
+.. automodule:: potpyri.instruments.DEIMOS
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      DEIMOS
+
diff --git a/docs/source/api/generated/potpyri.instruments.F2.rst b/docs/source/api/generated/potpyri.instruments.F2.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.F2
+======================
+
+.. automodule:: potpyri.instruments.F2
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      F2
+
diff --git a/docs/source/api/generated/potpyri.instruments.FOURSTAR.rst b/docs/source/api/generated/potpyri.instruments.FOURSTAR.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.FOURSTAR
+============================
+
+.. automodule:: potpyri.instruments.FOURSTAR
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      FOURSTAR
+
diff --git a/docs/source/api/generated/potpyri.instruments.GMOS.rst b/docs/source/api/generated/potpyri.instruments.GMOS.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.GMOS
+========================
+
+.. automodule:: potpyri.instruments.GMOS
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      GMOS
+
diff --git a/docs/source/api/generated/potpyri.instruments.IMACS.rst b/docs/source/api/generated/potpyri.instruments.IMACS.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.IMACS
+=========================
+
+.. automodule:: potpyri.instruments.IMACS
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      IMACS
+
diff --git a/docs/source/api/generated/potpyri.instruments.LRIS.rst b/docs/source/api/generated/potpyri.instruments.LRIS.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.LRIS
+========================
+
+.. automodule:: potpyri.instruments.LRIS
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      LRIS
+
diff --git a/docs/source/api/generated/potpyri.instruments.MMIRS.rst b/docs/source/api/generated/potpyri.instruments.MMIRS.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.MMIRS
+=========================
+
+.. automodule:: potpyri.instruments.MMIRS
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      MMIRS
+
diff --git a/docs/source/api/generated/potpyri.instruments.MOSFIRE.rst b/docs/source/api/generated/potpyri.instruments.MOSFIRE.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.MOSFIRE
+===========================
+
+.. automodule:: potpyri.instruments.MOSFIRE
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      MOSFIRE
+
diff --git a/docs/source/api/generated/potpyri.instruments.instrument.rst b/docs/source/api/generated/potpyri.instruments.instrument.rst
@@ -0,0 +1,12 @@
+potpyri.instruments.instrument
+==============================
+
+.. automodule:: potpyri.instruments.instrument
+
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      Instrument
+
diff --git a/docs/source/api/generated/potpyri.primitives.absphot.rst b/docs/source/api/generated/potpyri.primitives.absphot.rst
@@ -0,0 +1,18 @@
+potpyri.primitives.absphot
+==========================
+
+.. automodule:: potpyri.primitives.absphot
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      find_zeropoint
+
+   .. rubric:: Classes
+
+   .. autosummary::
+
+      absphot
+
diff --git a/docs/source/api/generated/potpyri.primitives.calibration.rst b/docs/source/api/generated/potpyri.primitives.calibration.rst
@@ -0,0 +1,14 @@
+potpyri.primitives.calibration
+==============================
+
+.. automodule:: potpyri.primitives.calibration
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      do_bias
+      do_dark
+      do_flat
+
diff --git a/docs/source/api/generated/potpyri.primitives.image_procs.rst b/docs/source/api/generated/potpyri.primitives.image_procs.rst
@@ -0,0 +1,22 @@
+potpyri.primitives.image\_procs
+===============================
+
+.. automodule:: potpyri.primitives.image_procs
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      add_stack_mask
+      align_images
+      create_error
+      create_mask
+      detrend_stack
+      generate_wcs
+      get_fieldcenter
+      image_proc
+      mask_satellites
+      remove_pv_distortion
+      stack_data
+
diff --git a/docs/source/api/generated/potpyri.primitives.photometry.rst b/docs/source/api/generated/potpyri.primitives.photometry.rst
@@ -0,0 +1,21 @@
+potpyri.primitives.photometry
+=============================
+
+.. automodule:: potpyri.primitives.photometry
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      create_conv
+      create_params
+      do_phot
+      extract_aperture_stats
+      extract_fwhm_from_epsf
+      generate_epsf
+      get_star_catalog
+      photloop
+      run_photometry
+      run_sextractor
+
diff --git a/docs/source/api/generated/potpyri.primitives.solve_wcs.rst b/docs/source/api/generated/potpyri.primitives.solve_wcs.rst
@@ -0,0 +1,15 @@
+potpyri.primitives.solve\_wcs
+=============================
+
+.. automodule:: potpyri.primitives.solve_wcs
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      align_to_gaia
+      clean_up_astrometry
+      get_gaia_catalog
+      solve_astrometry
+
diff --git a/docs/source/api/generated/potpyri.primitives.sort_files.rst b/docs/source/api/generated/potpyri.primitives.sort_files.rst
@@ -0,0 +1,19 @@
+potpyri.primitives.sort\_files
+==============================
+
+.. automodule:: potpyri.primitives.sort_files
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      handle_files
+      is_bad
+      is_bias
+      is_dark
+      is_flat
+      is_science
+      is_spec
+      sort_files
+
diff --git a/docs/source/api/generated/potpyri.scripts.archives.download_anet_index.rst b/docs/source/api/generated/potpyri.scripts.archives.download_anet_index.rst
@@ -0,0 +1,15 @@
+potpyri.scripts.archives.download\_anet\_index
+==============================================
+
+.. automodule:: potpyri.scripts.archives.download_anet_index
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      add_options
+      download_index_files
+      main
+      parse_astrometry_config
+
diff --git a/docs/source/api/generated/potpyri.scripts.archives.download_gemini_data.rst b/docs/source/api/generated/potpyri.scripts.archives.download_gemini_data.rst
@@ -0,0 +1,21 @@
+potpyri.scripts.archives.download\_gemini\_data
+===============================================
+
+.. automodule:: potpyri.scripts.archives.download_gemini_data
+
+
+   .. rubric:: Functions
+
+   .. autosummary::
+
+      add_options
+      download_data
+      download_file
+      get_associated_cals
+      get_full_outname
+      get_observation_data
+      load_cookie
+      main
+      mask_object_spectral_observation
+      unpack_tarfile
+