Working toward pip-installation.

MANIFEST.in

@@ -1,39 +1,18 @@
 include README.rst
-include CHANGES.rst
-
-include ah_bootstrap.py
 include setup.cfg
+include pyproject.toml
+include requirements.txt
+include environment.yml
+include contributors.md
 include popsycle/tests/coveragerc
 
-recursive-include popsycle *.pyx *.c *.pxd
+recursive-include popsycle *.py *.npz *.yaml *.rst
 recursive-include docs *
 recursive-include licenses *
-recursive-include cextern *
-recursive-include scripts *
 
 prune build
+prune dist
 prune docs/_build
 prune docs/api
 
-
-# the next few stanzas are for astropy_helpers.  It's derived from the
-# astropy_helpers/MANIFEST.in, but requires additional includes for the actual
-# package directory and egg-info.
-
-include astropy_helpers/README.rst
-include astropy_helpers/CHANGES.rst
-include astropy_helpers/LICENSE.rst
-recursive-include astropy_helpers/licenses *
-
-include astropy_helpers/ah_bootstrap.py
-
-recursive-include astropy_helpers/astropy_helpers *.py *.pyx *.c *.h *.rst
-recursive-include astropy_helpers/astropy_helpers.egg-info *
-# include the sphinx stuff with "*" because there are css/html/rst/etc.
-recursive-include astropy_helpers/astropy_helpers/sphinx *
-
-prune astropy_helpers/build
-prune astropy_helpers/astropy_helpers/tests
-
-
 global-exclude *.pyc *.o

README.rst

@@ -26,13 +26,68 @@ found at our galaxia GitHub repo: https://github.com/jluastro/galaxia.
 Installation
 ------------
 
-To install PopSyCLE, clone the GitHub repository and add the repository's
-path to your `PYTHONPATH`. For example:
+PopSyCLE is packaged and can be installed directly with either conda or pip.
+For the full pipeline, use **Python 3.11**. This is the compatible overlap for
+the current SPISEA and BAGLE dependency stack.
+
+Conda installation
+^^^^^^^^^^^^^^^^^^
+
+The repository ships with an ``environment.yml`` that installs the Python
+dependencies and installs PopSyCLE in editable mode.
+
+.. code-block:: bash
+
+    git clone https://github.com/MovingUniverseLab/PopSyCLE.git
+    cd PopSyCLE
+    conda env create -f environment.yml
+    conda activate popsycle
+
+Pip installation
+^^^^^^^^^^^^^^^^
+
+If you prefer virtual environments or already manage Python outside conda,
+install PopSyCLE directly with pip:
 
 .. code-block:: bash
 
-    git clone git@github.com:jluastro/PopSyCLE.git
-    echo "export PYTHONPATH=$PWD/PopSyCLE:$PYTHONPATH" >> ~/.bashrc
+    git clone https://github.com/MovingUniverseLab/PopSyCLE.git
+    cd PopSyCLE
+    python3.11 -m venv .venv
+    source .venv/bin/activate
+    python -m pip install --upgrade pip
+    python -m pip install -e .
+
+SPISEA
+^^^^^^
+
+SPISEA is still distributed upstream as a source checkout rather than a normal
+PyPI package, so install it separately after creating the PopSyCLE environment.
+Follow the SPISEA repository instructions and make sure it is importable in the
+same environment before running the PopSyCLE pipeline.
+
+.. code-block:: bash
+
+    git clone https://github.com/astropy/SPISEA.git
+    export PYTHONPATH=$PWD/SPISEA:$PYTHONPATH
+
+Command line entry point
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+After installation, the pipeline CLI is available as:
+
+.. code-block:: bash
+
+    popsycle --help
+
+Galaxia
+^^^^^^^
+
+Galaxia is still a separate external dependency and must be installed manually.
+PopSyCLE checks for the custom ``galaxia`` executable in ``$PATH`` and requires
+version ``0.7.2.1`` from the PopSyCLE-compatible Galaxia fork. Follow the
+Galaxia instructions in the documentation before running the synthesis
+pipeline.
 
 Running PopSyCLE
 ----------------

docs/source/popsycle_docs.rst

@@ -9,6 +9,9 @@ Documentation
 1 Installation
 ==============
 
+For a full-featured installation, use Python 3.11. That is the supported
+overlap for the current SPISEA and BAGLE dependency stack.
+
 1.1 Installing Galaxia
 -----------------------
 
@@ -82,17 +85,43 @@ Documentation
 1.2 Installing SPISEA
 ----------------------
 
-    SPISEA can be installed by cloning the repository from `<https://github.com/astropy/SPISEA>`_ and following the instructions.
+    SPISEA still needs to be installed separately from source. Use the
+    repository at `<https://github.com/astropy/SPISEA>`_ and make sure it is
+    importable in the same Python environment as PopSyCLE before running the
+    full pipeline.
 
 1.3 Installing BAGLE
 ----------------------
 
-    BAGLE can be installed by cloning the repository from `<https://github.com/MovingUniverseLab/BAGLE_Microlensing>`_ and following the instructions.
+    BAGLE is installed automatically as part of the packaged PopSyCLE install
+    methods below. If you need to install it separately, see
+    `<https://github.com/MovingUniverseLab/BAGLE_Microlensing>`_.
 
 1.4 Installing Python libraries
 --------------------------------
 
-    We recommend the Anaconda distribution. See `requirements.txt <https://github.com/jluastro/PopSyCLE/blob/main/requirements.txt>`_ for details.
+    We recommend one of the following installation flows from the repository
+    root.
+
+    Conda:
+
+    .. code-block:: bash
+
+        conda env create -f environment.yml
+        conda activate popsycle
+
+    Pip:
+
+    .. code-block:: bash
+
+        python3.11 -m venv .venv
+        source .venv/bin/activate
+        python -m pip install --upgrade pip
+        python -m pip install -e .
+
+    SPISEA still needs to be installed separately from its source repository
+    and made importable in the same environment. After PopSyCLE and SPISEA are
+    installed, the PopSyCLE CLI is available as ``popsycle``.
 
 ===============
 2 Reading Files
@@ -1325,4 +1354,3 @@ Note: be careful with the branch of arctangent. Practically, use ``numpy.arctan2
    :align: center
 
 Diagram of Heliocentric and Galactic coordinate systems. The red dot is the sun.
-

environment.yml

@@ -0,0 +1,26 @@
+name: popsycle
+channels:
+  - conda-forge
+dependencies:
+  - python=3.11
+  - pip
+  - numpy>=1.24.3
+  - matplotlib>=3.7.1
+  - astropy>=5.3
+  - h5py>=3.8.0
+  - scipy>=1.10.1
+  - pyyaml>=6.0
+  - pandas>=1.5.2
+  - pysynphot>=2.0.0
+  - synphot>=1.7.0
+  - stsynphot>=1.5.1
+  - scikit-learn
+  - celerite
+  - jplephem
+  - ephem
+  - pytest>=7.2.0
+  - numpydoc>=1.5
+  - sphinx_rtd_theme
+  - pip:
+      - --editable .
+# Install SPISEA separately in this environment after creation.

popsycle/run.py

@@ -12,16 +12,49 @@
 import sys
 import time
 import glob
-from popsycle import synthetic
-from popsycle import utils
-from popsycle.synthetic import _check_run_galaxia
-from popsycle.synthetic import _check_perform_pop_syn
-from popsycle.synthetic import _check_calc_events
-from popsycle.synthetic import _check_refine_events
-from popsycle.synthetic import _check_refine_binary_events
-from popsycle.synthetic import multiplicity_list
-from popsycle import binary_utils
-from popsycle import phot_utils
+
+synthetic = None
+utils = None
+binary_utils = None
+phot_utils = None
+_check_run_galaxia = None
+_check_perform_pop_syn = None
+_check_calc_events = None
+_check_refine_events = None
+_check_refine_binary_events = None
+multiplicity_list = None
+
+
+def _load_runtime_dependencies():
+    global synthetic
+    global utils
+    global binary_utils
+    global phot_utils
+    global _check_run_galaxia
+    global _check_perform_pop_syn
+    global _check_calc_events
+    global _check_refine_events
+    global _check_refine_binary_events
+    global multiplicity_list
+
+    if synthetic is not None:
+        return
+
+    from popsycle import synthetic as synthetic_mod
+    from popsycle import utils as utils_mod
+    from popsycle import binary_utils as binary_utils_mod
+    from popsycle import phot_utils as phot_utils_mod
+
+    synthetic = synthetic_mod
+    utils = utils_mod
+    binary_utils = binary_utils_mod
+    phot_utils = phot_utils_mod
+    _check_run_galaxia = synthetic_mod._check_run_galaxia
+    _check_perform_pop_syn = synthetic_mod._check_perform_pop_syn
+    _check_calc_events = synthetic_mod._check_calc_events
+    _check_refine_events = synthetic_mod._check_refine_events
+    _check_refine_binary_events = synthetic_mod._check_refine_binary_events
+    multiplicity_list = synthetic_mod.multiplicity_list
 
 
 def _return_filename_dict(output_root, filter_dict, red_law, multiplicity = None):
@@ -1356,6 +1389,7 @@ def main():
                           help="Skip running refine_binary_events.",
                           action='store_true')
     args = parser.parse_args()
+    _load_runtime_dependencies()
 
     run(output_root=args.output_root,
         field_config_filename=args.field_config_filename,

pyproject.toml

@@ -1,7 +1,10 @@
 [build-system]
 
-requires = ["setuptools",
-            "setuptools_scm",
+requires = ["setuptools>=64",
+            "setuptools_scm[toml]>=8",
             "wheel"]
 
 build-backend = 'setuptools.build_meta'
+
+[tool.setuptools_scm]
+write_to = "popsycle/version.py"

requirements.txt

@@ -11,8 +11,11 @@ pandas~=1.5.2
 numpydoc~=1.5
 sphinx_rtd_theme
 pysynphot
+synphot
+stsynphot
 scikit-learn
 # The following are needed for BAGLE
 celerite
 jplephem
 ephem
+bagle>=1.0.5

setup.cfg

@@ -4,30 +4,65 @@ author = Casey Lam and Jessica Lu
 author_email = jlu.astro@berkeley.edu
 license = BSD 3-Clause
 license_file = licenses/LICENSE.rst
-url = https://github.com/jluastro/PopSyCLE
+url = https://github.com/MovingUniverseLab/PopSyCLE
 description = Population Synthesis for Compact-object Lensing Events
 long_description = file: README.rst
 long_description_content_type = text/x-rst
 edit_on_github = False
-github_project = jluastro/PopSyCLE
+github_project = MovingUniverseLab/PopSyCLE
 
 [options]
 zip_safe = False
 packages = find:
-python_requires = >=3.6
-setup_requires = setuptools_scm
+include_package_data = True
+python_requires = >=3.11,<3.12
 install_requires =
-    astropy
+    numpy>=1.24.3
+    matplotlib>=3.7.1
+    astropy>=5.3
+    h5py>=3.8.0
+    scipy>=1.10.1
+    pyyaml>=6.0
+    pandas>=1.5.2
+    pysynphot>=2.0.0
+    synphot>=1.7.0
+    stsynphot>=1.5.1
+    scikit-learn
+    celerite
+    jplephem
+    ephem
+    bagle>=1.0.5
 
 
 [options.extras_require]
 test =
+    pytest>=7.2.0
     pytest-astropy
 docs =
+    numpydoc>=1.5
+    sphinx_rtd_theme
     sphinx-astropy
+dev =
+    build
+    wheel
+    twine
+
+[options.entry_points]
+console_scripts =
+    popsycle = popsycle.run:main
 
 [options.package_data]
-popsycle = data/*
+popsycle =
+    data/*
+    tests/data_correct/*
+    tests/data_test/*
+
+[options.packages.find]
+namespaces = False
+exclude =
+    popsycle.data
+    popsycle.tests.data_correct
+    popsycle.tests.data_test
 
 [tool:pytest]
 testpaths = "popsycle" "docs"