Dev

.github/workflows/cd.yaml

@@ -23,14 +23,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
         with:
           fetch-depth: 0
 
       - name: Build sdist and wheel
         run: pipx run build
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v5
         with:
           path: dist
 
@@ -45,11 +45,11 @@ jobs:
     permissions:
       id-token: write
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: "3.10"
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v6
         with:
           name: artifact
           path: dist
@@ -58,7 +58,7 @@ jobs:
           ls -ltrh
           ls -ltrh dist
       - name: Publish to Test PyPI
-        uses: pypa/gh-action-pypi-publish@v1.12.4
+        uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           repository-url: https://test.pypi.org/legacy/
           verbose: true
@@ -91,10 +91,10 @@ jobs:
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v6
         with:
           name: artifact
           path: dist
 
-      - uses: pypa/gh-action-pypi-publish@v1.12.4
+      - uses: pypa/gh-action-pypi-publish@v1.13.0
         if: startsWith(github.ref, 'refs/tags')

.github/workflows/coverage.yaml

@@ -20,7 +20,7 @@ jobs:
     steps:
       - uses: actions/checkout@master
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.10"
       - name: Record State
@@ -44,12 +44,23 @@ jobs:
           python -m pip install pytest-github-actions-annotate-failures
       - name: Install AstroPhot
         run: |
-          pip install -e .
+          pip install -e ".[dev]"
           pip show ${{ env.PROJECT_NAME }}
         shell: bash
-      - name: Test with pytest
+      - name: Test with pytest [torch]
         run: |
-          pytest -vvv --cov=${{ env.PROJECT_NAME }} --cov-report=xml --cov-report=term tests/
+          coverage run --source=${{ env.PROJECT_NAME }} -m pytest tests/
+        shell: bash
+        env:
+          CASKADE_BACKEND: torch
+      - name: Extra coverage report for jax checks
+        run: |
+          echo "Running extra coverage report for jax checks"
+          coverage run --append --source=${{ env.PROJECT_NAME }} -m pytest tests/
+        shell: bash
+        env:
+          JAX_ENABLE_X64: True
+          CASKADE_BACKEND: jax
 
       - name: Upload coverage reports to Codecov with GitHub Action
         uses: codecov/codecov-action@v5

.github/workflows/testing.yaml

@@ -15,12 +15,12 @@ jobs:
     runs-on: ${{matrix.os}}
     strategy:
       matrix:
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-latest, windows-latest, macOS-latest]
     steps:
       - uses: actions/checkout@master
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
       - name: Record State
@@ -35,12 +35,13 @@ jobs:
           python -m pip install --upgrade pip
           pip install pytest
           pip install wheel
+          pip install jax
           if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
         shell: bash
       - name: Install AstroPhot
         run: |
           cd $GITHUB_WORKSPACE/
-          pip install .
+          pip install .[dev]
           pip show astrophot
         shell: bash
       - name: Test with pytest

.gitignore

@@ -14,7 +14,7 @@ tests/*.yaml
 docs/source/tutorials/*.fits
 docs/source/tutorials/*.yaml
 docs/source/tutorials/*.jpg
-docs/autophot.*rst
+docs/source/astrophotdocs/*.ipynb
 docs/modules.rst
 pip_cheatsheet.txt
 .gitpod.yml

.readthedocs.yaml

@@ -20,11 +20,14 @@ sphinx:
 build:
   os: "ubuntu-20.04"
   tools:
-    python: "3.9"
+    python: "3.12"
   apt_packages:
     - pandoc # Specify pandoc to be installed via apt-get
+    - graphviz
   jobs:
     pre_build:
+      # Build docstring jupyter notebooks
+      - "python make_docs.py"
       # Generate the Sphinx configuration for this Jupyter Book so it builds.
       - "jupyter-book config sphinx docs/source/"
       # Create font cache ahead of jupyter book

astrophot/__init__.py

@@ -1,8 +1,28 @@
 import argparse
 import requests
 import torch
-from .parse_config import galfit_config, basic_config
-from . import models, image, plots, utils, fit, param, AP_config
+from . import config, models, plots, utils, fit, image, errors
+from .param import forward, Param, Module
+
+from .image import (
+    Image,
+    ImageList,
+    TargetImage,
+    TargetImageList,
+    SIPModelImage,
+    SIPTargetImage,
+    CMOSModelImage,
+    CMOSTargetImage,
+    JacobianImage,
+    JacobianImageList,
+    PSFImage,
+    ModelImage,
+    ModelImageList,
+    Window,
+    WindowList,
+)
+from .models import Model
+from .backend_obj import backend, ArrayLike
 
 try:
     from ._version import version as VERSION  # noqa
@@ -21,32 +41,10 @@
 
 def run_from_terminal() -> None:
     """
-    Execute AstroPhot from the command line with various options.
-
-    This function uses the `argparse` module to parse command line arguments and execute the appropriate functionality.
-    It accepts the following arguments:
-
-    - `filename`: the path to the configuration file. Or just 'tutorial' to download tutorials.
-    - `--config`: the type of configuration file being provided. One of: astrophot, galfit.
-    - `-v`, `--version`: print the current AstroPhot version to screen.
-    - `--log`: set the log file name for AstroPhot. Use 'none' to suppress the log file.
-    - `-q`: quiet flag to stop command line output, only print to log file.
-    - `--dtype`: set the float point precision. Must be one of: float64, float32.
-    - `--device`: set the device for AstroPhot to use for computations. Must be one of: cpu, gpu.
-
-    If the `filename` argument is not provided, it raises a `RuntimeError`.
-    If the `filename` argument is `tutorial` or `tutorials`,
-    it downloads tutorials from various URLs and saves them locally.
-
-    This function logs messages using the `AP_config` module,
-    which sets the logging output based on the `--log` and `-q` arguments.
-    The `dtype` and `device` of AstroPhot can also be set using the `--dtype` and `--device` arguments, respectively.
-
-    Returns:
-        None
+    Running from terminal no longer supported. This is only used for convenience to download the tutorials.
 
     """
-    AP_config.ap_logger.debug("running from the terminal, not sure if it will catch me.")
+    config.logger.debug("running from the terminal, not sure if it will catch me.")
     parser = argparse.ArgumentParser(
         prog="astrophot",
         description="Fast and flexible astronomical image photometry package. For the documentation go to: https://astrophot.readthedocs.io",
@@ -58,60 +56,60 @@ def run_from_terminal() -> None:
         metavar="configfile",
         help="the path to the configuration file. Or just 'tutorial' to download tutorials.",
     )
-    parser.add_argument(
-        "--config",
-        type=str,
-        default="astrophot",
-        choices=["astrophot", "galfit"],
-        metavar="format",
-        help="The type of configuration file being being provided. One of: astrophot, galfit.",
-    )
+    # parser.add_argument(
+    #     "--config",
+    #     type=str,
+    #     default="astrophot",
+    #     choices=["astrophot", "galfit"],
+    #     metavar="format",
+    #     help="The type of configuration file being being provided. One of: astrophot, galfit.",
+    # )
     parser.add_argument(
         "-v",
         "--version",
         action="version",
         version=f"%(prog)s {__version__}",
         help="print the current AstroPhot version to screen",
     )
-    parser.add_argument(
-        "--log",
-        type=str,
-        metavar="logfile.log",
-        help="set the log file name for AstroPhot. use 'none' to suppress the log file.",
-    )
-    parser.add_argument(
-        "-q",
-        action="store_true",
-        help="quiet flag to stop command line output, only print to log file",
-    )
-    parser.add_argument(
-        "--dtype",
-        type=str,
-        choices=["float64", "float32"],
-        metavar="datatype",
-        help="set the float point precision. Must be one of: float64, float32",
-    )
-    parser.add_argument(
-        "--device",
-        type=str,
-        choices=["cpu", "gpu"],
-        metavar="device",
-        help="set the device for AstroPhot to use for computations. Must be one of: cpu, gpu",
-    )
+    # parser.add_argument(
+    #     "--log",
+    #     type=str,
+    #     metavar="logfile.log",
+    #     help="set the log file name for AstroPhot. use 'none' to suppress the log file.",
+    # )
+    # parser.add_argument(
+    #     "-q",
+    #     action="store_true",
+    #     help="quiet flag to stop command line output, only print to log file",
+    # )
+    # parser.add_argument(
+    #     "--dtype",
+    #     type=str,
+    #     choices=["float64", "float32"],
+    #     metavar="datatype",
+    #     help="set the float point precision. Must be one of: float64, float32",
+    # )
+    # parser.add_argument(
+    #     "--device",
+    #     type=str,
+    #     choices=["cpu", "gpu"],
+    #     metavar="device",
+    #     help="set the device for AstroPhot to use for computations. Must be one of: cpu, gpu",
+    # )
 
     args = parser.parse_args()
 
     if args.log is not None:
-        AP_config.set_logging_output(
+        config.set_logging_output(
             stdout=not args.q, filename=None if args.log == "none" else args.log
         )
     elif args.q:
-        AP_config.set_logging_output(stdout=not args.q, filename="AstroPhot.log")
+        config.set_logging_output(stdout=not args.q, filename="AstroPhot.log")
 
     if args.dtype is not None:
-        AP_config.dtype = torch.float64 if args.dtype == "float64" else torch.float32
+        config.DTYPE = torch.float64 if args.dtype == "float64" else torch.float32
     if args.device is not None:
-        AP_config.device = "cpu" if args.device == "cpu" else "cuda:0"
+        config.DEVICE = "cpu" if args.device == "cpu" else "cuda:0"
 
     if args.filename is None:
         raise RuntimeError(
@@ -128,7 +126,6 @@ def run_from_terminal() -> None:
             "https://raw.github.com/Autostronomy/AstroPhot/main/docs/source/tutorials/BasicPSFModels.ipynb",
             "https://raw.github.com/Autostronomy/AstroPhot/main/docs/source/tutorials/AdvancedPSFModels.ipynb",
             "https://raw.github.com/Autostronomy/AstroPhot/main/docs/source/tutorials/ConstrainedModels.ipynb",
-            "https://raw.github.com/Autostronomy/AstroPhot-tutorials/main/docs/tutorials/simple_config.py",
         ]
         for url in tutorials:
             try:
@@ -140,12 +137,41 @@ def run_from_terminal() -> None:
                     f"WARNING: couldn't find tutorial: {url[url.rfind('/')+1:]} check internet connection"
                 )
 
-        AP_config.ap_logger.info("collected the tutorials")
-    elif args.config == "astrophot":
-        basic_config(args.filename)
-    elif args.config == "galfit":
-        galfit_config(args.filename)
+        config.logger.info("collected the tutorials")
     else:
-        raise ValueError(
-            f"Unrecognized configuration file format {args.config}. Should be one of: astrophot, galfit"
-        )
+        raise ValueError(f"Unrecognized request")
+
+
+__all__ = (
+    "models",
+    "image",
+    "Model",
+    "Image",
+    "ImageList",
+    "TargetImage",
+    "TargetImageList",
+    "SIPModelImage",
+    "SIPTargetImage",
+    "CMOSModelImage",
+    "CMOSTargetImage",
+    "JacobianImage",
+    "JacobianImageList",
+    "PSFImage",
+    "ModelImage",
+    "ModelImageList",
+    "Window",
+    "WindowList",
+    "plots",
+    "utils",
+    "fit",
+    "forward",
+    "Param",
+    "errors",
+    "Module",
+    "config",
+    "backend",
+    "run_from_terminal",
+    "__version__",
+    "__author__",
+    "__email__",
+)