diffsky 0.3.2__tar.gz → 0.3.4__tar.gz

{diffsky-0.3.2 → diffsky-0.3.4}/.github/workflows/mock_generation_test.yaml

@@ -23,7 +23,7 @@ jobs:
           remove_dotnet: true
           remove_haskell: true
           rm_cmd: "rmz"
-    
+
       - uses: actions/checkout@v6
         with:
           fetch-depth: 0
@@ -71,7 +71,7 @@ jobs:
 
           # Download data
           cd dsps_drn
-          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_lgmet_age.h5
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_emlines.hdf5
           cd filters
           wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_u_transmission.h5
           wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_g_transmission.h5
@@ -86,14 +86,14 @@ jobs:
           export DSPS_DRN="${GITHUB_WORKSPACE}/dsps_drn"
           echo "DSPS_DRN=${DSPS_DRN}" >> $GITHUB_ENV
 
-      - name: run mock generation script
+      - name: create mock with sfh_model option
         shell: bash -l {0}
         run: |
           # Create output directory
           mkdir -p ci_test_output
 
           # Run mock production script
-          mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_ou26_mock.py \
+          mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_ou26_mock_batch.py \
             poboy \
             0.01 \
             0.2 \
@@ -101,7 +101,6 @@ jobs:
             1 \
             ci_test_output \
             ci_test_mock \
-            -fn_u_params sfh_model \
             -sfh_model smdpl_dr1 \
             -synthetic_cores 1 \
             -lgmp_min 12.0 \
@@ -111,10 +110,87 @@ jobs:
       - name: verify script completed
         shell: bash -l {0}
         run: |
-          echo "Mock generation script completed successfully"
+          echo "sfh_model mock generated successfully"
 
       - name: validate mock
         shell: bash -l {0}
         run: |
-          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/synthetic_cores/smdpl_dr1
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/smdpl_dr1
+
+      - name: remove sfh_model mock
+        shell: bash -l {0}
+        run: |
+          rm -rf ci_test_output
+
+      - name: create mock with cosmos_fit option
+        shell: bash -l {0}
+        run: |
+          # Create output directory
+          mkdir -p ci_test_output
+
+          # Run mock production script
+          mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_ou26_mock_batch.py \
+            poboy \
+            0.01 \
+            0.2 \
+            0 \
+            1 \
+            ci_test_output \
+            ci_test_mock \
+            -cosmos_fit cosmos_260120_UM \
+            -synthetic_cores 1 \
+            -lgmp_min 12.0 \
+            -lgmp_max 13.0 \
+            --lsst_only
+
+      - name: verify script completed
+        shell: bash -l {0}
+        run: |
+          echo "sfh_model mock generated successfully"
+
+      - name: validate mock
+        shell: bash -l {0}
+        run: |
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/cosmos_260120_UM
+
+      - name: remove cosmos_fit mock
+        shell: bash -l {0}
+        run: |
+          rm -rf ci_test_output
+
+      - name: create mock with no_dbk option
+        shell: bash -l {0}
+        run: |
+          # Create output directory
+          mkdir -p ci_test_output
+
+          # Run mock production script
+          mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_ou26_mock_batch.py \
+            poboy \
+            0.01 \
+            0.2 \
+            0 \
+            1 \
+            ci_test_output \
+            ci_test_mock \
+            -cosmos_fit cosmos_260120_UM \
+            -synthetic_cores 1 \
+            -lgmp_min 12.0 \
+            -lgmp_max 13.0 \
+            --lsst_only --no_dbk
+
+      - name: verify script completed
+        shell: bash -l {0}
+        run: |
+          echo "sfh_model mock generated successfully"
+
+      - name: validate mock
+        shell: bash -l {0}
+        run: |
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/cosmos_260120_UM --no_dbk
+
+      - name: remove cosmos_fit mock
+        shell: bash -l {0}
+        run: |
+          rm -rf ci_test_output
 

diffsky-0.3.4/.github/workflows/shape_optimization.yaml

@@ -0,0 +1,85 @@
+name: Test script for optimizing galaxy shapes
+
+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:
+  mock-generation:
+    name: python fit_bulge_shapes_to_rp13.py
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - name: free disk space
+        uses: endersonmenezes/free-disk-space@v3
+        with:
+          remove_android: true
+          remove_dotnet: true
+          remove_haskell: true
+          rm_cmd: "rmz"
+
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          python-version: 3.11
+          channels: conda-forge
+          channel-priority: strict
+          show-channel-urls: true
+          miniforge-version: latest
+
+      - name: configure conda and install code
+        shell: bash -l {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.CPAC_PRIVATE_REPO_TOKEN }}
+          GITHUB_USER: ${{ secrets.GH_USR_TESTING_TOKEN }}
+
+        run: |
+          conda config --set always_yes yes
+          conda install --quiet \
+            --file=requirements.txt
+          conda install --quiet \
+            pip \
+            setuptools \
+            "setuptools_scm>=7,<8" \
+            matplotlib \
+            astropy \
+            h5py \
+            mpi4py \
+            mpich
+          conda uninstall diffmah --force
+          conda uninstall diffstar --force
+          conda uninstall dsps --force
+          pip install --no-deps --no-build-isolation git+https://github.com/ArgonneCPAC/diffmah.git
+          pip install --no-deps --no-build-isolation git+https://github.com/ArgonneCPAC/diffstar.git
+          pip install --no-deps --no-build-isolation git+https://github.com/ArgonneCPAC/dsps.git
+          python -m pip install --no-build-isolation --no-deps -e .
+
+      - name: run disk optimization script
+        shell: bash -l {0}
+        run: |
+          python scripts/ellipsoid_shape_fitting/fit_disk_shapes_to_rp13.py -nsteps 20
+
+      - name: verify disk script completed
+        shell: bash -l {0}
+        run: |
+          echo "Disk optimization script completed successfully"
+
+      - name: run bulge optimization script
+        shell: bash -l {0}
+        run: |
+          python scripts/ellipsoid_shape_fitting/fit_bulge_shapes_to_rp13.py -nsteps 20
+
+      - name: verify bulge script completed
+        shell: bash -l {0}
+        run: |
+          echo "Bulge optimization script completed successfully"
+

{diffsky-0.3.2 → diffsky-0.3.4}/.github/workflows/test_main_branch.yaml

@@ -45,6 +45,7 @@ jobs:
             setuptools \
             "setuptools_scm>=7,<8" \
             matplotlib \
+            scipy \
             astropy \
             python-build
           pip uninstall diffmah --yes

{diffsky-0.3.2 → diffsky-0.3.4}/.github/workflows/tests_cron.yaml

@@ -50,6 +50,7 @@ jobs:
             "setuptools_scm>=7,<8" \
             matplotlib \
             astropy \
+            readme_renderer \
             python-build
           pip uninstall diffmah --yes
           pip uninstall diffstar --yes

{diffsky-0.3.2 → diffsky-0.3.4}/.gitignore

@@ -12,6 +12,7 @@ scripts/*.cfg
 scripts/*.cfg~
 
 .DS_Store
+**/.DS_Store
 
 docs/source/drn_dsps_temp/*
 

{diffsky-0.3.2 → diffsky-0.3.4}/CHANGES.rst

@@ -1,3 +1,33 @@
+0.3.4 (2026-02-05)
+-------------------
+- Reduce mock filesize by 10x by omitting redundant dust parameters (https://github.com/ArgonneCPAC/diffsky/pull/317)
+- Add feature to make mocks with/out disk/bulge/knot decomposition (https://github.com/ArgonneCPAC/diffsky/pull/317)
+- Require Numpy>=2 (https://github.com/ArgonneCPAC/diffsky/pull/331)
+- Include emission line fluxes in output mock (https://github.com/ArgonneCPAC/diffsky/pull/335)
+- Mock galaxies populating both synthetic and simulated halos are written out to the same directory (https://github.com/ArgonneCPAC/diffsky/pull/336)
+
+
+0.3.3 (2026-01-06)
+-------------------
+- Fix bug in elliptical projections
+    - https://github.com/ArgonneCPAC/diffsky/pull/297
+- Reoptimize disk/bulge shapes
+    - https://github.com/ArgonneCPAC/diffsky/pull/301
+- Implement automated plot-generating scripts comparing cosmos to different diffsky models
+    - https://github.com/ArgonneCPAC/diffsky/pull/291
+- Improve bookkeeping in cross-matching jobs
+    - https://github.com/ArgonneCPAC/diffsky/pull/293
+    - https://github.com/ArgonneCPAC/diffsky/pull/294
+    - https://github.com/ArgonneCPAC/diffsky/pull/299
+    - https://github.com/ArgonneCPAC/diffsky/pull/300
+- Compute photometry in batches when making mocks
+    - https://github.com/ArgonneCPAC/diffsky/pull/295
+- Adopt astropy units in mock metadata
+    - https://github.com/ArgonneCPAC/diffsky/pull/303
+- Add peculiar velocities to output mock
+    - https://github.com/ArgonneCPAC/diffsky/pull/304
+
+
 0.3.2 (2025-12-04)
 -------------------
 - Resolve bug in the treatment of scatter in the SSP errors.

{diffsky-0.3.2 → diffsky-0.3.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffsky
-Version: 0.3.2
+Version: 0.3.4
 Summary: Library for differentiable generation of synthetic skies
 Author-email: Andrew Hearin <ahearin@anl.gov>
 License: BSD 3-Clause License
@@ -38,7 +38,7 @@ Classifier: Programming Language :: Python :: 3
 Requires-Python: >=3.11
 Description-Content-Type: text/x-rst
 License-File: LICENSE.rst
-Requires-Dist: numpy
+Requires-Dist: numpy>=2
 Requires-Dist: jax
 Requires-Dist: diffmah>=0.7.3
 Requires-Dist: diffstar>=1.0.1

diffsky-0.3.4/diffsky/_version.py

@@ -0,0 +1 @@
+__version__ = '0.3.4'

{diffsky-0.3.2 → diffsky-0.3.4}/diffsky/burstpop/diagnostics/plot_fburstpop.py

@@ -1,10 +1,17 @@
 """ """
 
 import numpy as np
-from matplotlib import pyplot as plt
 
 from ..fburstpop import DEFAULT_FBURSTPOP_PARAMS, get_lgfburst_from_fburstpop_params
 
+try:
+    from matplotlib import pyplot as plt
+
+    HAS_MATPLOTLIB = True
+except ImportError:
+    HAS_MATPLOTLIB = False
+MATPLOTLIB_MSG = "Must have matplotlib installed to use this function"
+
 
 def make_fburstpop_comparison_plot(
     params,
@@ -28,6 +35,8 @@ def make_fburstpop_comparison_plot(
         filename of the output figure
 
     """
+    assert HAS_MATPLOTLIB, MATPLOTLIB_MSG
+
     nsm, nsfr = 250, 250
     logsm_grid = np.linspace(7, 12, nsm)
     logssfr_grid = np.linspace(-13, -8, nsfr)

{diffsky-0.3.2 → diffsky-0.3.4}/diffsky/burstpop/diagnostics/plot_tburstpop.py

@@ -2,11 +2,18 @@
 
 import numpy as np
 from dsps.sfh import diffburst
-from matplotlib import lines as mlines
-from matplotlib import pyplot as plt
 
 from .. import tburstpop as tbp
 
+try:
+    from matplotlib import lines as mlines
+    from matplotlib import pyplot as plt
+
+    HAS_MATPLOTLIB = True
+except ImportError:
+    HAS_MATPLOTLIB = False
+MATPLOTLIB_MSG = "Must have matplotlib installed to use this function"
+
 
 def make_tburstpop_comparison_plot(
     params,
@@ -30,6 +37,7 @@ def make_tburstpop_comparison_plot(
         filename of the output figure
 
     """
+    assert HAS_MATPLOTLIB, MATPLOTLIB_MSG
     lgyrarr = np.linspace(5, 9.05, 100)
 
     logsmarr = np.array((9.0, 9.0, 12.0, 12.0))

{diffsky-0.3.2 → diffsky-0.3.4}/diffsky/burstpop/diagnostics/tests/test_plot_fburstpop.py

@@ -2,11 +2,19 @@
 
 import os
 
-from ..plot_fburstpop import DEFAULT_FBURSTPOP_PARAMS, make_fburstpop_comparison_plot
+import pytest
+
+from ..plot_fburstpop import (
+    DEFAULT_FBURSTPOP_PARAMS,
+    HAS_MATPLOTLIB,
+    MATPLOTLIB_MSG,
+    make_fburstpop_comparison_plot,
+)
 
 _THIS_DRNAME = os.path.dirname(os.path.abspath(__file__))
 
 
+@pytest.mark.skipif(not HAS_MATPLOTLIB, reason=MATPLOTLIB_MSG)
 def test_make_freqburst_comparison_plot():
     fn = os.path.join(_THIS_DRNAME, "dummy.png")
     make_fburstpop_comparison_plot(DEFAULT_FBURSTPOP_PARAMS, fname=fn)

{diffsky-0.3.2 → diffsky-0.3.4}/diffsky/burstpop/diagnostics/tests/test_plot_tburstpop.py

@@ -2,12 +2,19 @@
 
 import os
 
+import pytest
+
 from ... import tburstpop as tbp
-from ..plot_tburstpop import make_tburstpop_comparison_plot
+from ..plot_tburstpop import (
+    HAS_MATPLOTLIB,
+    MATPLOTLIB_MSG,
+    make_tburstpop_comparison_plot,
+)
 
 _THIS_DRNAME = os.path.dirname(os.path.abspath(__file__))
 
 
+@pytest.mark.skipif(not HAS_MATPLOTLIB, reason=MATPLOTLIB_MSG)
 def test_make_freqburst_comparison_plot():
     fn = os.path.join(_THIS_DRNAME, "dummy.png")
     make_tburstpop_comparison_plot(tbp.DEFAULT_TBURSTPOP_PARAMS, fname=fn)

diffsky-0.3.4/diffsky/data_loaders/__init__.py

@@ -0,0 +1,6 @@
+""""""
+
+# flake8: noqa
+
+from .io_utils import load_flat_hdf5
+from .load_ssp_data import load_fake_ssp_data, load_ssp_templates

{diffsky-0.3.2 → diffsky-0.3.4}/diffsky/data_loaders/cosmos20_loader.py

@@ -13,6 +13,15 @@ except ImportError:
     HAS_ASTROPY = False
 
 
+Z_MIN, Z_MAX = 0.4, 2.5
+
+HSC_MAG_NAMES = ["HSC_g_MAG", "HSC_r_MAG", "HSC_i_MAG", "HSC_z_MAG", "HSC_y_MAG"]
+UVISTA_MAG_NAMES = ["UVISTA_Y_MAG", "UVISTA_J_MAG", "UVISTA_H_MAG", "UVISTA_Ks_MAG"]
+COSMOS_TARGET_MAGS = [*HSC_MAG_NAMES, *UVISTA_MAG_NAMES]
+MAGI_THRESH = 25.5
+
+NANFILL = -999.0
+
 COSMOS20_BASENAME = "COSMOS2020_Farmer_processed_hlin.fits"
 
 SKY_AREA = 1.21  # square degrees
@@ -103,4 +112,85 @@ def load_cosmos20(
     else:
         return cat
 
-    return cat
+
+def apply_nan_cuts(cosmos, mag_names=COSMOS_TARGET_MAGS):
+    """Remove any galaxy with a NaN in any column storing a target magnitude
+
+    Parameters
+    ----------
+    cosmos : astropy Table
+
+    mag_names : list of strings
+
+    Returns
+    -------
+    cosmos : astropy Table
+        Catalog after applying a NaN cut on `photoz` and any colname in mag_names
+
+    """
+    msk_has_nan = np.isnan(cosmos["photoz"])
+    for name in mag_names:
+        x = np.nan_to_num(
+            cosmos[name], copy=True, nan=NANFILL, posinf=NANFILL, neginf=NANFILL
+        )
+        msk_has_nan = msk_has_nan | (x == NANFILL)
+
+    cosmos = cosmos[~msk_has_nan]
+    return cosmos
+
+
+def get_is_complete_mask(cosmos, z_min=Z_MIN, z_max=Z_MAX, magi_thresh=MAGI_THRESH):
+    """Compute mask to define the redshift and i-mag threshold for our target data
+
+    Parameters
+    ----------
+    cosmos : astropy Table
+
+    z_min, z_max : float
+        Galaxies outside this range will be excluded
+
+    magi_thresh : float
+        Galaxies fainter than this apparent magnitude will be excluded
+
+    Returns
+    -------
+    msk_is_complete : array, dtype bool
+        Boolean mask defining galaxies that pass the completeness cut
+
+    """
+    msk_redshift = (cosmos["photoz"] > z_min) & (cosmos["photoz"] < z_max)
+    msk_i_thresh = cosmos["HSC_i_MAG"] < magi_thresh
+    msk_is_complete = msk_redshift & msk_i_thresh
+    return msk_is_complete
+
+
+def get_color_outlier_mask(cosmos, mag_names, p_cut=0.5):
+    """Compute mask to define extreme outliers in color space
+
+    Parameters
+    ----------
+    cosmos : astropy Table
+
+    mag_names : list of strings
+        Column names defining the colors for which outliers will be excluded
+
+    p_cut : float, optional
+        Value in the range [0, 100] defining a percentile cut
+
+    Returns
+    -------
+    msk_is_not_outlier : array, dtype bool
+        Boolean mask defining galaxies that pass the outlier cut
+
+    """
+    msk_is_outlier = np.zeros(len(cosmos)).astype(bool)
+    for name0, name1 in zip(mag_names[0:], mag_names[1:]):
+        c0 = cosmos[name0]
+        c1 = cosmos[name1]
+        color = c0 - c1
+        lo, hi = np.percentile(color, (p_cut, 100.0 - p_cut))
+        msk_is_outlier = msk_is_outlier | (color < lo) | (color > hi)
+
+    msk_is_not_outlier = ~msk_is_outlier
+
+    return msk_is_not_outlier