diffsky 0.1.0__tar.gz → 0.1.2__tar.gz

{diffsky-0.1.0 → diffsky-0.1.2}/.github/workflows/linting.yml

@@ -16,7 +16,7 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
           channels: conda-forge,defaults
           channel-priority: strict
           show-channel-urls: true

diffsky-0.1.2/.github/workflows/monthly-warning-test.yml

@@ -0,0 +1,58 @@
+name: Test for Warnings
+
+on:
+  workflow_dispatch: null
+  schedule:
+    # Runs "First of every month at 3:15am Central"
+    - cron: '15 8 1 * *'
+
+jobs:
+  tests:
+    name: tests
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.11
+          channels: conda-forge,defaults
+          channel-priority: strict
+          show-channel-urls: true
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          use-mamba: true
+
+      - name: configure conda and install code
+      # Test against current main branch of all diff+ dependencies
+        shell: bash -l {0}
+        run: |
+          conda config --set always_yes yes
+          mamba install --quiet \
+            --file=requirements.txt
+          mamba install -y -q \
+            flake8 \
+            pytest \
+            pytest-xdist \
+            pytest-cov \
+            pip \
+            setuptools \
+            "setuptools_scm>=7,<8" \
+            matplotlib \
+            python-build
+          pip uninstall diffmah --yes
+          pip uninstall diffstar --yes
+          pip uninstall dsps --yes
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffmah.git
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffstar.git
+          pip install --no-deps git+https://github.com/ArgonneCPAC/dsps.git
+          python -m pip install --no-build-isolation --no-deps -e .
+
+      - name: test that no warnings are raised
+        shell: bash -l {0}
+        run: |
+          export PYTHONWARNINGS=error
+          pytest -v diffsky --cov --cov-report=xml

{diffsky-0.1.0 → diffsky-0.1.2}/.github/workflows/tests.yml

@@ -1,4 +1,4 @@
-name: tests
+name: test-latest-diffstuff-releases
 
 on:
   push:
@@ -18,7 +18,7 @@ jobs:
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.9
+          python-version: 3.11
           channels: conda-forge,defaults
           channel-priority: strict
           show-channel-urls: true
@@ -27,6 +27,7 @@ jobs:
           use-mamba: true
 
       - name: configure conda and install code
+      # Test against conda-forge for all dependencies except use main branch for dsps
         shell: bash -l {0}
         run: |
           conda config --set always_yes yes
@@ -40,7 +41,10 @@ jobs:
             pip \
             setuptools \
             "setuptools_scm>=7,<8" \
+            matplotlib \
             python-build
+          pip uninstall dsps --yes
+          pip install --no-deps git+https://github.com/ArgonneCPAC/dsps.git
           python -m pip install --no-build-isolation --no-deps -e .
 
       - name: test

diffsky-0.1.2/.github/workflows/tests_cron.yml

@@ -0,0 +1,88 @@
+name: test-main-branch-diffstuff
+
+on:
+  workflow_dispatch: null
+  schedule:
+    # Runs "every Monday & Thursday at 3:05am Central"
+    - cron: '5 8 * * 1,4'
+  push:
+    branches:
+      - main
+  pull_request: null
+
+jobs:
+  tests:
+    name: tests
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: 3.11
+          channels: conda-forge,defaults
+          channel-priority: strict
+          show-channel-urls: true
+          miniforge-version: latest
+          miniforge-variant: Mambaforge
+          use-mamba: true
+
+      - name: configure conda and install code
+      # Test against current main branch of all diff+ dependencies
+        shell: bash -l {0}
+        run: |
+          conda config --set always_yes yes
+          mamba install --quiet \
+            --file=requirements.txt
+          mamba install -y -q \
+            flake8 \
+            pytest \
+            pytest-xdist \
+            pytest-cov \
+            pip \
+            setuptools \
+            "setuptools_scm>=7,<8" \
+            matplotlib \
+            python-build
+          pip uninstall diffmah --yes
+          pip uninstall diffstar --yes
+          pip uninstall dsps --yes
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffmah.git
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffstar.git
+          pip install --no-deps git+https://github.com/ArgonneCPAC/dsps.git
+          python -m pip install --no-build-isolation --no-deps -e .
+
+      - name: test
+        shell: bash -l {0}
+        run: |
+          pytest -v diffsky --cov --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+
+      - name: test versions
+        shell: bash -el {0}
+        run: |
+          pip uninstall diffsky --yes
+          [[ $(python setup.py --version) != "0.0.0" ]] || exit 1
+
+          rm -rf dist/*
+          python setup.py sdist
+          pip install --no-deps --no-build-isolation dist/*.tar.gz
+          pushd ..
+          python -c "import diffsky; assert diffsky.__version__ != '0.0.0'"
+          popd
+          pip uninstall diffsky --yes
+
+          rm -rf dist/*
+          python -m build --sdist . --outdir dist
+          pip install --no-deps --no-build-isolation dist/*.tar.gz
+          pushd ..
+          python -c "import diffsky; assert diffsky.__version__ != '0.0.0'"
+          popd
+          pip uninstall diffsky --yes
+
+          python -m pip install -v --no-deps --no-build-isolation -e .

diffsky-0.1.2/CHANGES.rst

@@ -0,0 +1,13 @@
+0.1.2 (2024-10-25)
+-------------------
+- Update calls to diffmah v0.6.1 and diffstar v0.3.2
+
+
+0.1.1 (2023-10-04)
+-------------------
+- Update calls to dsps v0.3.4
+
+
+0.1.0 (2023-10-03)
+-------------------
+- First release. Compatible with diffstar v0.2.1 and dsps v0.3.3.

{diffsky-0.1.0 → diffsky-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: diffsky
-Version: 0.1.0
+Version: 0.1.2
 Summary: Library for differentiable generation of synthetic skies
 Author-email: Andrew Hearin <ahearin@anl.gov>
 License: BSD 3-Clause License
@@ -35,28 +35,28 @@ License: BSD 3-Clause License
         
 Project-URL: home, https://github.com/ArgonneCPAC/diffsky
 Classifier: Programming Language :: Python :: 3
-Requires-Python: >=3.9
+Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
 Requires-Dist: numpy
 Requires-Dist: jax
-Requires-Dist: h5py
-Requires-Dist: diffmah
-Requires-Dist: diffstar
+Requires-Dist: diffmah>=0.6.1
+Requires-Dist: diffstar>=0.3.2
 Requires-Dist: dsps
+Requires-Dist: h5py
 
 diffsky
 ============
 
-Code for producing mock catalogs based on 
+Diffsky is a python library based on JAX for producing mock catalogs based on 
 `diffstar <https://diffstar.readthedocs.io/en/latest/>`_ 
 and `dsps <https://dsps.readthedocs.io/en/latest/>`_.
 
 Installation
 ------------
-The latest release of diffsky is available for installation with pip or conda::
+The latest release of diffsky is available for installation with pip or conda-forge::
 
-    $ conda install diffsky
+    $ conda install -c conda-forge diffsky
 
 
 To install diffsky into your environment from the source code::
@@ -67,9 +67,9 @@ To install diffsky into your environment from the source code::
 
 Conda environment
 ~~~~~~~~~~~~~~~~~
-For a typical development environment in conda::
+For a typical development environment in conda-forge::
 
-    $ conda create -n diffsky_env python=3.9 numpy jax pytest ipython jupyter matplotlib scipy h5py diffmah diffstar dsps diffsky
+    $ conda create -c conda-forge -n diffsky_env python=3.11 numpy jax pytest ipython jupyter matplotlib scipy h5py diffmah diffstar dsps diffsky
 
 
 Documentation

{diffsky-0.1.0 → diffsky-0.1.2}/README.rst

@@ -1,15 +1,15 @@
 diffsky
 ============
 
-Code for producing mock catalogs based on 
+Diffsky is a python library based on JAX for producing mock catalogs based on 
 `diffstar <https://diffstar.readthedocs.io/en/latest/>`_ 
 and `dsps <https://dsps.readthedocs.io/en/latest/>`_.
 
 Installation
 ------------
-The latest release of diffsky is available for installation with pip or conda::
+The latest release of diffsky is available for installation with pip or conda-forge::
 
-    $ conda install diffsky
+    $ conda install -c conda-forge diffsky
 
 
 To install diffsky into your environment from the source code::
@@ -20,9 +20,9 @@ To install diffsky into your environment from the source code::
 
 Conda environment
 ~~~~~~~~~~~~~~~~~
-For a typical development environment in conda::
+For a typical development environment in conda-forge::
 
-    $ conda create -n diffsky_env python=3.9 numpy jax pytest ipython jupyter matplotlib scipy h5py diffmah diffstar dsps diffsky
+    $ conda create -c conda-forge -n diffsky_env python=3.11 numpy jax pytest ipython jupyter matplotlib scipy h5py diffmah diffstar dsps diffsky
 
 
 Documentation

{diffsky-0.1.0 → diffsky-0.1.2}/diffsky/__init__.py

@@ -1,5 +1,7 @@
 """
 """
+
 # flake8: noqa
 
 from ._version import __version__
+from .mass_functions.mc_diffmah_tpeak import mc_subhalos

diffsky-0.1.2/diffsky/_version.py

@@ -0,0 +1 @@
+__version__ = '0.1.2'

diffsky-0.1.2/diffsky/burstpop/__init__.py

@@ -0,0 +1,11 @@
+"""
+"""
+# flake8: noqa
+
+from .diffburstpop import (
+    DEFAULT_DIFFBURSTPOP_PARAMS,
+    DEFAULT_DIFFBURSTPOP_U_PARAMS,
+    calc_bursty_age_weights_from_diffburstpop_params,
+    get_bounded_diffburstpop_params,
+    get_unbounded_diffburstpop_params,
+)

diffsky-0.1.2/diffsky/burstpop/diagnostics/plot_fburstpop.py

@@ -0,0 +1,60 @@
+"""
+"""
+
+import numpy as np
+from matplotlib import pyplot as plt
+
+from ..fburstpop import DEFAULT_FBURSTPOP_PARAMS, get_lgfburst_from_fburstpop_params
+
+
+def make_fburstpop_comparison_plot(
+    params,
+    params2=DEFAULT_FBURSTPOP_PARAMS,
+    fname=None,
+    label1=r"${\rm new\ model}$",
+    label2=r"${\rm default\ model}$",
+):
+    """Make basic diagnostic plot of the model for Fburst
+
+    Parameters
+    ----------
+    params : namedtuple
+        Instance of fburstpop.FburstPopParams
+
+    params2 : namedtuple, optional
+        Instance of fburstpop.FburstPopParams
+        Default is set by DEFAULT_FBURSTPOP_PARAMS
+
+    fname : string, optional
+        filename of the output figure
+
+    """
+    nsm, nsfr = 250, 250
+    logsm_grid = np.linspace(7, 12, nsm)
+    logssfr_grid = np.linspace(-13, -8, nsfr)
+
+    X, Y = np.meshgrid(logsm_grid, logssfr_grid)
+
+    Z = get_lgfburst_from_fburstpop_params(params, X, Y)
+    Z2 = get_lgfburst_from_fburstpop_params(params2, X, Y)
+
+    fig, axes = plt.subplots(1, 2, figsize=(10, 4))
+    (ax0, ax1) = axes
+
+    pcm0 = ax0.pcolor(X, Y, Z, cmap="coolwarm_r", vmin=-4.5, vmax=-2.1)
+    fig.colorbar(pcm0, ax=ax0)
+
+    pcm1 = ax1.pcolor(X, Y, Z2, cmap="coolwarm_r", vmin=-4.5, vmax=-2.1)
+    fig.colorbar(pcm1, ax=ax1, label=r"${\rm lgFburst}$")
+    for ax in axes:
+        xlabel = ax.set_xlabel(r"$\log_{10}M_{\star}/M_{\odot}$")
+    ylabel = ax0.set_ylabel(r"${\rm \log_{10}sSFR}$")
+
+    ax0.set_title(label1)
+    ax1.set_title(label2)
+
+    if fname is not None:
+        fig.savefig(
+            fname, bbox_extra_artists=[xlabel, ylabel], bbox_inches="tight", dpi=200
+        )
+    return fig

diffsky-0.1.2/diffsky/burstpop/diagnostics/tests/test_plot_fburstpop.py

@@ -0,0 +1,15 @@
+"""
+"""
+
+import os
+
+from ..plot_fburstpop import DEFAULT_FBURSTPOP_PARAMS, make_fburstpop_comparison_plot
+
+_THIS_DRNAME = os.path.dirname(os.path.abspath(__file__))
+
+
+def test_make_freqburst_comparison_plot():
+    fn = os.path.join(_THIS_DRNAME, "dummy.png")
+    make_fburstpop_comparison_plot(DEFAULT_FBURSTPOP_PARAMS, fname=fn)
+    assert os.path.isfile(fn)
+    os.remove(fn)

diffsky-0.1.2/diffsky/burstpop/diffburstpop.py

@@ -0,0 +1,87 @@
+"""
+"""
+from collections import namedtuple
+
+from dsps.sfh.diffburst import BurstParams, calc_bursty_age_weights
+from jax import jit as jjit
+
+from .fburstpop import (
+    DEFAULT_FBURSTPOP_PARAMS,
+    get_bounded_fburstpop_params,
+    get_lgfburst_from_fburstpop_params,
+    get_unbounded_fburstpop_params,
+)
+from .tburstpop import (
+    DEFAULT_TBURSTPOP_PARAMS,
+    get_bounded_tburstpop_params,
+    get_tburst_params_from_tburstpop_params,
+    get_unbounded_tburstpop_params,
+)
+
+DiffburstPopParams = namedtuple(
+    "DiffburstPopParams", ["fburstpop_params", "tburstpop_params"]
+)
+DEFAULT_DIFFBURSTPOP_PARAMS = DiffburstPopParams(
+    DEFAULT_FBURSTPOP_PARAMS, DEFAULT_TBURSTPOP_PARAMS
+)
+_BURSTPOP_UPNAMES = [
+    key.replace("params", "u_params") for key in DEFAULT_DIFFBURSTPOP_PARAMS._fields
+]
+DiffburstPopUParams = namedtuple("DiffburstPopUParams", _BURSTPOP_UPNAMES)
+
+
+@jjit
+def get_bounded_diffburstpop_params(u_params):
+    u_fburstpop_params, u_tburstpop_params = u_params
+    bounded_tburstpop_params = get_bounded_tburstpop_params(u_tburstpop_params)
+    bounded_fburstpop_params = get_bounded_fburstpop_params(u_fburstpop_params)
+    diffburstpop_params = DiffburstPopParams(
+        bounded_fburstpop_params, bounded_tburstpop_params
+    )
+    return diffburstpop_params
+
+
+@jjit
+def get_unbounded_diffburstpop_params(params):
+    fburstpop_params, tburstpop_params = params
+    unbounded_fburstpop_params = get_unbounded_fburstpop_params(fburstpop_params)
+    unbounded_tburstpop_params = get_unbounded_tburstpop_params(tburstpop_params)
+    diffburstpop_u_params = DiffburstPopUParams(
+        unbounded_fburstpop_params, unbounded_tburstpop_params
+    )
+    return diffburstpop_u_params
+
+
+@jjit
+def calc_bursty_age_weights_from_diffburstpop_params(
+    diffburstpop_params, logsm, logssfr, ssp_lg_age_gyr, smooth_age_weights
+):
+    lgfburst = get_lgfburst_from_fburstpop_params(
+        diffburstpop_params.fburstpop_params, logsm, logssfr
+    )
+
+    tburst_params = get_tburst_params_from_tburstpop_params(
+        diffburstpop_params.tburstpop_params, logsm, logssfr
+    )
+    lgyr_peak, lgyr_max = tburst_params
+    burst_params = BurstParams(lgfburst, lgyr_peak, lgyr_max)
+
+    age_weights = calc_bursty_age_weights(
+        burst_params, smooth_age_weights, ssp_lg_age_gyr
+    )
+
+    return age_weights, burst_params
+
+
+def calc_bursty_age_weights_from_diffburstpop_u_params(
+    diffburstpop_u_params, logsm, logssfr, ssp_lg_age_gyr, smooth_age_weights
+):
+    diffburstpop_params = get_bounded_diffburstpop_params(diffburstpop_u_params)
+    args = diffburstpop_params, logsm, logssfr, ssp_lg_age_gyr, smooth_age_weights
+    age_weights, burst_params = calc_bursty_age_weights_from_diffburstpop_params(*args)
+    return age_weights, burst_params
+
+
+DEFAULT_DIFFBURSTPOP_U_PARAMS = DiffburstPopUParams(
+    *get_unbounded_diffburstpop_params(DEFAULT_DIFFBURSTPOP_PARAMS)
+)

diffsky-0.1.2/diffsky/burstpop/diffqburstpop.py

@@ -0,0 +1,97 @@
+"""
+"""
+
+from collections import namedtuple
+
+from dsps.sfh.diffburst import BurstParams, calc_bursty_age_weights
+from jax import jit as jjit
+
+from .fburstpop import (
+    DEFAULT_FBURSTPOP_PARAMS,
+    get_bounded_fburstpop_params,
+    get_lgfburst_from_fburstpop_params,
+    get_unbounded_fburstpop_params,
+)
+from .freqburst import (
+    DEFAULT_FREQBURST_PARAMS,
+    get_bounded_freqburst_params,
+    get_unbounded_freqburst_params,
+)
+from .tburstpop import (
+    DEFAULT_TBURSTPOP_PARAMS,
+    get_bounded_tburstpop_params,
+    get_tburst_params_from_tburstpop_params,
+    get_unbounded_tburstpop_params,
+)
+
+DiffburstPopParams = namedtuple(
+    "DiffburstPopParams", ["freqburst_params", "fburstpop_params", "tburstpop_params"]
+)
+DEFAULT_DIFFBURSTPOP_PARAMS = DiffburstPopParams(
+    DEFAULT_FREQBURST_PARAMS, DEFAULT_FBURSTPOP_PARAMS, DEFAULT_TBURSTPOP_PARAMS
+)
+_BURSTPOP_UPNAMES = [
+    key.replace("params", "u_params") for key in DEFAULT_DIFFBURSTPOP_PARAMS._fields
+]
+DiffburstPopUParams = namedtuple("DiffburstPopUParams", _BURSTPOP_UPNAMES)
+
+
+@jjit
+def get_bounded_diffburstpop_params(u_params):
+    u_freqburst_params, u_fburstpop_params, u_tburstpop_params = u_params
+    bounded_freqburst_params = get_bounded_freqburst_params(u_freqburst_params)
+    bounded_tburstpop_params = get_bounded_tburstpop_params(u_tburstpop_params)
+    bounded_fburstpop_params = get_bounded_fburstpop_params(u_fburstpop_params)
+    diffburstpop_params = DiffburstPopParams(
+        bounded_freqburst_params, bounded_fburstpop_params, bounded_tburstpop_params
+    )
+    return diffburstpop_params
+
+
+@jjit
+def get_unbounded_diffburstpop_params(params):
+    freqburst_params, fburstpop_params, tburstpop_params = params
+    unbounded_freqburst_params = get_unbounded_freqburst_params(freqburst_params)
+    unbounded_fburstpop_params = get_unbounded_fburstpop_params(fburstpop_params)
+    unbounded_tburstpop_params = get_unbounded_tburstpop_params(tburstpop_params)
+    diffburstpop_u_params = DiffburstPopUParams(
+        unbounded_freqburst_params,
+        unbounded_fburstpop_params,
+        unbounded_tburstpop_params,
+    )
+    return diffburstpop_u_params
+
+
+@jjit
+def calc_bursty_age_weights_from_diffburstpop_params(
+    diffburstpop_params, logsm, logssfr, ssp_lg_age_gyr, smooth_age_weights
+):
+    lgfburst = get_lgfburst_from_fburstpop_params(
+        diffburstpop_params.fburstpop_params, logsm, logssfr
+    )
+
+    tburst_params = get_tburst_params_from_tburstpop_params(
+        diffburstpop_params.tburstpop_params, logsm, logssfr
+    )
+    lgyr_peak, lgyr_max = tburst_params
+    burst_params = BurstParams(lgfburst, lgyr_peak, lgyr_max)
+
+    age_weights = calc_bursty_age_weights(
+        burst_params, smooth_age_weights, ssp_lg_age_gyr
+    )
+
+    return age_weights, burst_params
+
+
+def calc_bursty_age_weights_from_diffburstpop_u_params(
+    diffburstpop_u_params, logsm, logssfr, ssp_lg_age_gyr, smooth_age_weights
+):
+    diffburstpop_params = get_bounded_diffburstpop_params(diffburstpop_u_params)
+    args = diffburstpop_params, logsm, logssfr, ssp_lg_age_gyr, smooth_age_weights
+    age_weights, burst_params = calc_bursty_age_weights_from_diffburstpop_params(*args)
+    return age_weights, burst_params
+
+
+DEFAULT_DIFFBURSTPOP_U_PARAMS = DiffburstPopUParams(
+    *get_unbounded_diffburstpop_params(DEFAULT_DIFFBURSTPOP_PARAMS)
+)