Merge pull request #265 from Autostronomy/getcaskade

Major update: convert to caksade parameter management system

Author: ConnorStoneAstro

.github/workflows/coverage.yaml

@@ -44,7 +44,7 @@ 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

.github/workflows/testing.yaml

@@ -15,7 +15,7 @@ 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
@@ -40,7 +40,7 @@ jobs:
       - name: Install AstroPhot
         run: |
           cd $GITHUB_WORKSPACE/
-          pip install .
+          pip install .[dev]
           pip show astrophot
         shell: bash
       - name: Test with pytest

.readthedocs.yaml

@@ -23,6 +23,7 @@ build:
     python: "3.9"
   apt_packages:
     - pandoc # Specify pandoc to be installed via apt-get
+    - graphviz
   jobs:
     pre_build:
       # Generate the Sphinx configuration for this Jupyter Book so it builds.

astrophot/__init__.py

@@ -1,8 +1,24 @@
 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
+from .param import forward, Param, Module
+
+from .image import (
+    Image,
+    ImageList,
+    TargetImage,
+    TargetImageList,
+    SIPTargetImage,
+    JacobianImage,
+    JacobianImageList,
+    PSFImage,
+    ModelImage,
+    ModelImageList,
+    Window,
+    WindowList,
+)
+from .models import Model
 
 try:
     from ._version import version as VERSION  # noqa
@@ -21,32 +37,10 @@
 
 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 +52,60 @@ 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 +122,6 @@ 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 +133,35 @@ 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",
+    "Model",
+    "Image",
+    "ImageList",
+    "TargetImage",
+    "TargetImageList",
+    "SIPTargetImage",
+    "JacobianImage",
+    "JacobianImageList",
+    "PSFImage",
+    "ModelImage",
+    "ModelImageList",
+    "Window",
+    "WindowList",
+    "plots",
+    "utils",
+    "fit",
+    "forward",
+    "Param",
+    "Module",
+    "config",
+    "run_from_terminal",
+    "__version__",
+    "__author__",
+    "__email__",
+)

astrophot/AP_config.py astrophot/config.pyastrophot/AP_config.py renamed to astrophot/config.py

@@ -2,29 +2,28 @@
 import logging
 import torch
 
-__all__ = ["ap_dtype", "ap_device", "ap_logger", "set_logging_output"]
+__all__ = ["DTYPE", "DEVICE", "logger", "set_logging_output"]
 
-ap_dtype = torch.float64
-ap_device = "cuda:0" if torch.cuda.is_available() else "cpu"
-ap_verbose = 0
+DTYPE = torch.float64
+DEVICE = "cuda:0" if torch.cuda.is_available() else "cpu"
 
 logging.basicConfig(
     filename="AstroPhot.log",
     level=logging.INFO,
     format="%(asctime)s:%(levelname)s: %(message)s",
 )
-ap_logger = logging.getLogger()
+logger = logging.getLogger()
 out_handler = logging.StreamHandler(sys.stdout)
 out_handler.setLevel(logging.INFO)
 out_handler.setFormatter(logging.Formatter("%(message)s"))
-ap_logger.addHandler(out_handler)
+logger.addHandler(out_handler)
 
 
 def set_logging_output(stdout=True, filename=None, **kwargs):
     """
     Change the logging system for AstroPhot.
     Here you can set whether output prints to screen or to a logging file.
-    This function will remove all handlers from the current logger in ap_logger,
+    This function will remove all handlers from the current logger in logger,
     then add new handlers based on the input to the function.
 
     Parameters:
@@ -39,20 +38,20 @@ def set_logging_output(stdout=True, filename=None, **kwargs):
 
     """
     hi = 0
-    while hi < len(ap_logger.handlers):
-        if isinstance(ap_logger.handlers[hi], logging.StreamHandler):
-            ap_logger.removeHandler(ap_logger.handlers[hi])
-        elif isinstance(ap_logger.handlers[hi], logging.FileHandler):
-            ap_logger.removeHandler(ap_logger.handlers[hi])
+    while hi < len(logger.handlers):
+        if isinstance(logger.handlers[hi], logging.StreamHandler):
+            logger.removeHandler(logger.handlers[hi])
+        elif isinstance(logger.handlers[hi], logging.FileHandler):
+            logger.removeHandler(logger.handlers[hi])
         else:
             hi += 1
 
     if stdout:
         out_handler = logging.StreamHandler(sys.stdout)
         out_handler.setLevel(kwargs.get("stdout_level", logging.INFO))
         out_handler.setFormatter(kwargs.get("stdout_formatter", logging.Formatter("%(message)s")))
-        ap_logger.addHandler(out_handler)
-        ap_logger.debug("logging now going to stdout")
+        logger.addHandler(out_handler)
+        logger.debug("logging now going to stdout")
     if filename is not None:
         out_handler = logging.FileHandler(filename)
         out_handler.setLevel(kwargs.get("filename_level", logging.INFO))
@@ -62,5 +61,5 @@ def set_logging_output(stdout=True, filename=None, **kwargs):
                 logging.Formatter("%(asctime)s:%(levelname)s: %(message)s"),
             )
         )
-        ap_logger.addHandler(out_handler)
-        ap_logger.debug("logging now going to %s" % filename)
+        logger.addHandler(out_handler)
+        logger.debug("logging now going to %s" % filename)

astrophot/errors/fit.py

@@ -1,11 +1,19 @@
 from .base import AstroPhotError
 
-__all__ = ("OptimizeStop",)
+__all__ = ("OptimizeStopFail", "OptimizeStopSuccess")
 
 
-class OptimizeStop(AstroPhotError):
+class OptimizeStopFail(AstroPhotError):
     """
-    Raised at any point to stop optimization process.
+    Raised at any point to stop optimization process due to failure.
+    """
+
+    pass
+
+
+class OptimizeStopSuccess(AstroPhotError):
+    """
+    Raised at any point to stop optimization process due to success condition.
     """
 
     pass

astrophot/fit/__init__.py

@@ -1,33 +1,9 @@
-from .base import *
-from .lm import *
-from .oldlm import *
-from .gradient import *
-from .iterative import *
-from .minifit import *
-
-try:
-    from .hmc import *
-    from .nuts import *
-except AssertionError as e:
-    print("Could not load HMC or NUTS due to:", str(e))
-from .mhmcmc import *
-
-"""
-base: This module defines the base class BaseOptimizer,
-      which is used as the parent class for all optimization algorithms in AstroPhot.
-      This module contains helper functions used across multiple optimization algorithms,
-      such as computing gradients and making copies of models.
-
-LM: This module defines the class LM,
-    which uses the Levenberg-Marquardt algorithm to perform optimization.
-    This algorithm adjusts the learning rate at each step to find the optimal value.
-
-Grad: This module defines the class Gradient-Optimizer,
-      which uses a simple gradient descent algorithm to perform optimization.
-      This algorithm adjusts the learning rate at each step to find the optimal value.
-
-Iterative: This module defines the class Iter,
-            which uses an iterative algorithm to perform Optimization.
-            This algorithm repeatedly fits each model individually until they all converge.
-
-"""
+from .lm import LM
+from .gradient import Grad
+from .iterative import Iter
+from .scipy_fit import ScipyFit
+from .minifit import MiniFit
+from .hmc import HMC
+from .mhmcmc import MHMCMC
+
+__all__ = ["LM", "Grad", "Iter", "ScipyFit", "MiniFit", "HMC", "MHMCMC"]