All tests pass, updated github workflow, some doc updates to be finis…

…hed later on

.github/workflows/python-package.yml

@@ -5,17 +5,17 @@ name: Python package
 
 on:
   push:
-    branches: [ master ]
-  pull_request:
-    branches: [ master ]
+    branches: [ implement_core_liger_datamodels ]
+  #pull_request:
+    #branches: [ master ]
 
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.11]
+        python-version: [3.12]
 
     steps:
     - uses: actions/checkout@v4
@@ -27,32 +27,34 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Install libcfitsio
-      run: sudo apt-get install libcfitsio-dev graphviz pandoc
-    - name: Install pip dependencies
-      run: |
-          python -m pip install -r requirements.txt -r test-requirements.txt
+    # - name: Install libcfitsio
+      # run: sudo apt-get install libcfitsio-dev graphviz pandoc
+    # - name: Install pip dependencies
+      # run: |
+          # python -m pip install -r requirements.txt -r test-requirements.txt
     - name: Setup CRDS
       run: |
         git clone --depth 1 https://github.com/oirlab/liger-iris-crds-cache $HOME/crds_cache
-    - name: Build and install
-      run: python setup.py build_ext -i && python setup.py install
-      env:
-          C_INCLUDE_PATH: /usr/include/cfitsio/
-    - name: Test
-      run: source setup_local_crds.sh && make test
-    - name: Build docs
-      if: ${{ matrix.python-version==3.11 }}
-      run: |
-          python -m pip install -r docs/requirements.txt && cd docs && make html
-    - name: Deploy
-      if: ${{ matrix.python-version==3.11 && contains(github.ref, 'master') }}
-      uses: JamesIves/github-pages-deploy-action@v4
-      with:
-        branch: master
-        folder: docs/_build/html
-        repository-name: oirlab/liger-iris-pipeline
-        token: ${{ secrets.PAT }}
+    #- name: Build and install
+      #run: python setup.py build_ext -i && python setup.py install
+      #env:
+          #C_INCLUDE_PATH: /usr/include/cfitsio/
+    # - name: Test
+      # run: source setup_local_crds.sh && make test
+    # - name: Build docs
+      # if: ${{ matrix.python-version==3.12 }}
+      # run: |
+          # python -m pip install -r docs/requirements.txt && cd docs && make html
+    # - name: Deploy
+    #   if: ${{ matrix.python-version==3.11 && contains(github.ref, 'master') }}
+    #   uses: JamesIves/github-pages-deploy-action@v4
+      # with:
+        # branch: master
+        # folder: docs/_build/html
+        # repository-name: oirlab/liger-iris-pipeline
+        # token: ${{ secrets.PAT }}
+    # ################################
+
       # the token expires every year, create a new Github Personal Access Token where:
       # resource owner is oirlab
       # repo is oirlab/liger-iris-pipeline (notice dashes, this is the docs repo)

docs/available-steps.rst

@@ -5,7 +5,7 @@ Available algorithms
    :maxdepth: 2
 
    dq_init/index.rst
-   background/index.rst
+   sky_subtraction/index.rst
    dark_subtraction/index.rst
    normalize/index.rst
    pipeline/index.rst

docs/conf.py

@@ -1,136 +1,67 @@
-# -*- coding: utf-8 -*-
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
+# Configuration file for the Sphinx documentation builder.
 #
-# Astropy documentation build configuration file.
-#
-# This file is execfile()d with the current directory set to its containing dir.
-#
-# Note that not all possible configuration values are present in this file.
-#
-# All configuration values have a default. Some values are defined in
-# the global Astropy configuration which is loaded here before anything else.
-# See astropy.sphinx.conf for which values are set there.
-
-# If extensions (or modules to document with autodoc) are in another directory,
-# add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-# sys.path.insert(0, os.path.abspath('..'))
-# IMPORTANT: the above commented section was generated by sphinx-quickstart, but
-# is *NOT* appropriate for astropy or Astropy affiliated packages. It is left
-# commented out with this explanation to make it clear why this should not be
-# done. If the sys.path entry above is added, when the astropy.sphinx.conf
-# import occurs, it will import the *source* version of astropy instead of the
-# version installed (if invoked as "make html" or directly with sphinx), or the
-# version in the build directory (if "python setup.py build_sphinx" is used).
-# Thus, any C-extensions that are needed to build the documentation will *not*
-# be accessible, and the documentation will not build correctly.
-
-import os
-import sys
-import datetime
-from importlib import import_module
-
-try:
-    from sphinx_astropy.conf.v1 import *  # noqa
-except ImportError:
-    print(
-        "ERROR: the documentation requires the sphinx-astropy package to be installed"
-    )
-    sys.exit(1)
-
-# Get configuration information from setup.cfg
-from configparser import ConfigParser
-
-conf = ConfigParser()
-
-conf.read([os.path.join(os.path.dirname(__file__), "..", "setup.cfg")])
-setup_cfg = dict(conf.items("metadata"))
-
-# -- General configuration ----------------------------------------------------
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-# By default, highlight as Python 3.
-highlight_language = "python3"
+import liger_iris_pipeline
 
-# If your documentation needs a minimal Sphinx version, state it here.
-# needs_sphinx = '1.2'
 
-# To perform a Sphinx version check that needs to be more specific than
-# major.minor, call `check_sphinx_version("x.y.z")` here.
-# check_sphinx_version("1.2.1")
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
-# List of patterns, relative to source directory, that match files and
-# directories to ignore when looking for source files.
-exclude_patterns.append("_templates")
+project = 'Liger IRIS DRS'
+copyright = '2025, Bryson Cale, Andrea Zonca, Shelley Wright'
+author = 'Bryson Cale, Andrea Zonca, Shelley Wright'
 
-# This is added to the end of RST files - a good place to put substitutions to
-# be used globally.
-rst_epilog += """
-"""
-
-# -- Project information ------------------------------------------------------
-
-# This does not *have* to match the package name, but typically does
-project = "liger_iris_pipeline"
-author = setup_cfg["author"]
-copyright = "{0}, {1}".format(datetime.datetime.now().year, setup_cfg["author"])
-
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-
-import_module(setup_cfg["name"])
-package = sys.modules[setup_cfg["name"]]
-
-# The short X.Y version.
-version = package.__version__.split("-", 1)[0]
-# The full version, including alpha/beta/rc tags.
-release = package.__version__
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
+extensions = [
+    'sphinx_automodapi.automodapi',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.imgmath',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'nbsphinx',
+]
 
-# -- Options for HTML output --------------------------------------------------
+templates_path = ['_templates']
+exclude_patterns = []
 
-# A NOTE ON HTML THEMES
-# The global astropy configuration uses a custom theme, 'bootstrap-astropy',
-# which is installed along with astropy. A different theme can be used or
-# the options for this theme can be modified by overriding some of the
-# variables set in the global configuration. The variables set in the
-# global configuration are listed below, commented out.
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
+html_theme = 'alabaster'
+html_static_path = ['_static']
 
-# Add any paths that contain custom themes here, relative to this directory.
-# To use a different custom theme, add the directory containing the theme.
-# html_theme_path = []
 
-# The theme to use for HTML and HTML Help pages.  See the documentation for
-# a list of builtin themes. To override the custom theme, set this to the
-# name of a builtin theme or the name of a custom theme in html_theme_path.
-# html_theme = None
+# Version
+version = liger_iris_pipeline.__version__
+# The full version, including alpha/beta/rc tags.
+#release = hispecdrp.__version__
 
-html_theme_options = {
-    "logotext1": "liger_iris_pipeline",  # white,  semi-bold
-    "logotext2": "",  # orange, light
-    "logotext3": ":docs",  # white,  light
-}
 
-# Custom sidebar templates, maps document names to template names.
-# html_sidebars = {}
+# By default, highlight as Python 3.
+highlight_language = "python3"
 
-# The name of an image file (relative to this directory) to place at the top
-# of the sidebar.
-# html_logo = ''
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+exclude_patterns = ['_templates']
 
-# The name of an image file (within the static path) to use as favicon of the
-# docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
-# pixels large.
-# html_favicon = ''
+# html_theme_options = {
+#     "logotext1": "liger_iris_pipeline",  # white,  semi-bold
+#     "logotext2": "",  # orange, light
+#     "logotext3": ":docs",  # white,  light
+# }
 
-# If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
-# using the given strftime format.
-# html_last_updated_fmt = ''
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-html_title = "{0} v{1}".format(project, release)
+html_title = f"Liger IRIS DRS v{liger_iris_pipeline.__version__}"
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = project + "doc"
@@ -149,22 +80,13 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [("index", project.lower(), project + u" Documentation", [author], 1)]
+# man_pages = [("index", project.lower(), project + u" Documentation", [author], 1)]
 
 
 # -- Options for the edit_on_github extension ---------------------------------
 
-if eval(setup_cfg.get("edit_on_github")):
-    extensions += ["sphinx_astropy.ext.edit_on_github"]
-
-    edit_on_github_project = setup_cfg["github_project"]
-    edit_on_github_branch = "master"
-
-    edit_on_github_source_root = ""
-    edit_on_github_doc_root = "docs"
-
 # -- Resolving issue number to links in changelog -----------------------------
-github_issues_url = "https://github.com/{0}/issues/".format(setup_cfg["github_project"])
+github_issues_url = "https://github.com/oirlab/liger_iris_pipeline/issues/"
 
 # -- Turn on nitpicky mode for sphinx (to warn about references not found) ----
 #
@@ -192,26 +114,21 @@
 #     target = target.strip()
 #     nitpick_ignore.append((dtype, six.u(target)))
 
-intersphinx_mapping = {"jwst": ("https://jwst-pipeline.readthedocs.io/en/latest", None)}
-
-latex_elements = {
-    # Additional stuff for the LaTeX preamble.
-    "preamble": "".join(
-        (
-            "\DeclareUnicodeCharacter{00A0}{ }",  # NO-BREAK SPACE
-            "\DeclareUnicodeCharacter{251C}{+}",  # BOX DRAWINGS LIGHT VERTICAL AND RIGHT
-            "\DeclareUnicodeCharacter{2514}{+}",  # BOX DRAWINGS LIGHT UP AND RIGHT
-        )
-    ),
+intersphinx_mapping = {
+    "jwst": ("https://jwst-pipeline.readthedocs.io/en/latest", None)
 }
 
-# Static files
-html_static_path = ['_static']
+# latex_elements = {
+#     # Additional stuff for the LaTeX preamble.
+#     "preamble": "".join(
+#         (
+#             "\DeclareUnicodeCharacter{00A0}{ }",  # NO-BREAK SPACE
+#             "\DeclareUnicodeCharacter{251C}{+}",  # BOX DRAWINGS LIGHT VERTICAL AND RIGHT
+#             "\DeclareUnicodeCharacter{2514}{+}",  # BOX DRAWINGS LIGHT UP AND RIGHT
+#         )
+#     ),
+# }
 
-extensions += [
-    "nbsphinx",
-    "sphinx.ext.mathjax",
-]
 nbsphinx_kernel_name = "python3"
 nbsphinx_timeout = 600
 nbsphinx_allow_errors = False

liger_iris_pipeline/associations/association_base.py

@@ -57,11 +57,17 @@ def from_product(cls, product : dict):
 
     @classmethod
     def from_member(cls, member : str | datamodels.LigerIRISDataModel):
+        if isinstance(member, str):
+            expname = member
+        elif isinstance(member, datamodels.LigerIRISDataModel) and member._filename is not None:
+            expname = member._filename
+        else:
+            expname = member # NOTE: This will break serialization
         input_model = datamodels.open(member)
         product = {
             "members": [
                 {
-                    "expname": input_model.filename,
+                    "expname": expname,
                     "exptype": input_model.meta.exposure.type,
                 },
             ]

liger_iris_pipeline/datamodels/model_base.py

@@ -19,6 +19,7 @@ def __init__(self, init=None, instrument : str | None = None, **kwargs):
 
         # Pass to super if already a datamodel, schema already known
         if isinstance(init, LigerIRISDataModel):
+            self.set_schema_from_instrument(instrument=init.instrument)
             super().__init__(init=init, **kwargs)
         else:
             # Get the schema from instrument name

liger_iris_pipeline/datamodels/utils.py

@@ -22,20 +22,20 @@ def open(init=None, memmap=False, **kwargs):
     Creates a DataModel from a number of different types.
 
     Parameters:
-    init:
-        - None: A default data model with no shape
-        - shape tuple: Initialize with empty data of the given shape
-        - file path: Initialize from the given file (FITS, JSON or ASDF)
-        - readable file object: Initialize from the given file object
-        - astropy.io.fits.HDUList: Initialize from the given `~astropy.io.fits.HDUList`.
-        - A numpy array: A new model with the data array initialized to what was passed in.
-        - dict: The object model tree for the data model
-    memmap: (bool) (Turn memmap of file on or off.  (default: False).
-    kwargs:
-        validate_arrays (bool): If `True`, arrays will be validated against ndim, max_ndim, and datatype validators in the schemas.
+        init:
+            - None: A default data model with no shape
+            - shape tuple: Initialize with empty data of the given shape
+            - file path: Initialize from the given file (FITS, JSON or ASDF)
+            - readable file object: Initialize from the given file object
+            - astropy.io.fits.HDUList: Initialize from the given `~astropy.io.fits.HDUList`.
+            - A numpy array: A new model with the data array initialized to what was passed in.
+            - dict: The object model tree for the data model
+        memmap: (bool) (Turn memmap of file on or off.  (default: False).
+        kwargs:
+            validate_arrays (bool): If `True`, arrays will be validated against ndim, max_ndim, and datatype validators in the schemas.
     
     Returns:
-    LigerIRISDataModel: The specific LigerIRISDataModel instance.
+        LigerIRISDataModel : The specific LigerIRISDataModel instance.
     """
 
     from .model_base import LigerIRISDataModel