diffsky 0.3.6__tar.gz → 0.3.7__tar.gz

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/linting.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: "ubuntu-latest"
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
 
       - uses: conda-incubator/setup-miniconda@v4
         with:

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/mockgen_opencosmo_main.yaml

@@ -15,6 +15,10 @@ jobs:
     name: python make_lj_mock.py testing_lj_mock_config.yaml
     runs-on: "ubuntu-latest"
 
+    env:
+      # Force UCX to use standard TCP/shared memory
+      UCX_TLS: "tcp,self,sm"
+
     steps:
       - name: free disk space
         uses: endersonmenezes/free-disk-space@v3
@@ -24,7 +28,7 @@ jobs:
           remove_haskell: true
           rm_cmd: "rmz"
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
@@ -88,19 +92,21 @@ jobs:
 
           # Download data
           cd dsps_drn
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_emlines.sparse.hdf5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/fsps_v0.4.7_mist_c3k_a_kroupa_wNE_logGasU-2.0_logGasZ0.0.sparse.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/ssp-data-v1/fsps_v0.4.7_mist_c3k_a_kroupa_wNE_logGasU-2.0_logGasZ0.0.sparse.h5
 
           cd filters
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_u_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_g_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_r_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_i_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_z_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_y_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_u_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_g_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_r_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_i_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_z_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_y_transmission.h5
           cd ..
           cd ..
 
+          # download lc_cores-decomposition.txt
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/hacc-data-lastjourney-v1/lc_cores-decomposition.txt
+
           # Set environment variable
           export DSPS_DRN="${GITHUB_WORKSPACE}/dsps_drn"
           echo "DSPS_DRN=${DSPS_DRN}" >> $GITHUB_ENV
@@ -114,6 +120,8 @@ jobs:
           # Run mock production script
           mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_lj_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
 
+          mv lc_cores-decomposition.txt ci_test_output/dummy_version_name/
+
       - name: verify script completed
         shell: bash -l {0}
         run: |
@@ -122,7 +130,7 @@ jobs:
       - name: validate mock
         shell: bash -l {0}
         run: |
-          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/dummy_version_name
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
 
       - name: Create dummy diffsky galaxies for OpenCosmo
         shell: bash -l {0}

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/mockgen_opencosmo_release.yaml

@@ -15,6 +15,10 @@ jobs:
     name: python make_lj_mock.py testing_lj_mock_config.yaml
     runs-on: "ubuntu-latest"
 
+    env:
+      # Force UCX to use standard TCP/shared memory
+      UCX_TLS: "tcp,self,sm"
+
     steps:
       - name: free disk space
         uses: endersonmenezes/free-disk-space@v3
@@ -24,7 +28,7 @@ jobs:
           remove_haskell: true
           rm_cmd: "rmz"
 
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
@@ -83,18 +87,21 @@ jobs:
 
           # Download data
           cd dsps_drn
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_emlines.sparse.hdf5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/fsps_v0.4.7_mist_c3k_a_kroupa_wNE_logGasU-2.0_logGasZ0.0.sparse.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/ssp-data-v1/fsps_v0.4.7_mist_c3k_a_kroupa_wNE_logGasU-2.0_logGasZ0.0.sparse.h5
+
           cd filters
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_u_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_g_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_r_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_i_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_z_transmission.h5
-          wget $WGET_OPTS https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_y_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_u_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_g_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_r_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_i_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_z_transmission.h5
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_y_transmission.h5
           cd ..
           cd ..
 
+          # download lc_cores-decomposition.txt
+          wget $WGET_OPTS https://github.com/ArgonneCPAC/diffsky-data/releases/download/hacc-data-lastjourney-v1/lc_cores-decomposition.txt
+
           # Set environment variable
           export DSPS_DRN="${GITHUB_WORKSPACE}/dsps_drn"
           echo "DSPS_DRN=${DSPS_DRN}" >> $GITHUB_ENV
@@ -108,6 +115,8 @@ jobs:
           # Run mock production script
           mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_lj_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
 
+          mv lc_cores-decomposition.txt ci_test_output/dummy_version_name/
+
       - name: verify script completed
         shell: bash -l {0}
         run: |
@@ -116,7 +125,7 @@ jobs:
       - name: validate mock
         shell: bash -l {0}
         run: |
-          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/dummy_version_name
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
 
       - name: Create dummy diffsky galaxies for OpenCosmo
         shell: bash -l {0}

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/monthly-warning-test.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: "ubuntu-latest"
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/test_latest_releases.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: "ubuntu-latest"
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
@@ -64,7 +64,7 @@ jobs:
           pytest -v diffsky --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v6
+        uses: codecov/codecov-action@v7
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/test_main_branch.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: "ubuntu-latest"
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
@@ -72,7 +72,7 @@ jobs:
           pytest -v diffsky --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v6
+        uses: codecov/codecov-action@v7
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/test_main_branch_no_extra_deps.yaml

@@ -17,7 +17,7 @@ jobs:
     runs-on: "ubuntu-latest"
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
@@ -75,7 +75,7 @@ jobs:
           pytest -v diffsky --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v6
+        uses: codecov/codecov-action@v7
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 

{diffsky-0.3.6 → diffsky-0.3.7}/.github/workflows/tests_cron.yaml

@@ -16,7 +16,7 @@ jobs:
     runs-on: "ubuntu-latest"
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
 
@@ -76,7 +76,7 @@ jobs:
           pytest -v diffsky --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v6
+        uses: codecov/codecov-action@v7
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 

{diffsky-0.3.6 → diffsky-0.3.7}/.gitignore

@@ -10,6 +10,7 @@ Untitled*.ipynb
 
 scripts/*.cfg
 scripts/*.cfg~
+docs/source/mock_download_dir
 
 .DS_Store
 **/.DS_Store
@@ -17,6 +18,7 @@ scripts/*.cfg~
 docs/source/drn_dsps_temp/*
 ci_test_output/*
 docs/source/download_dir/*
+docs/source/mock_download_dir/*
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

diffsky-0.3.7/.readthedocs.yml

@@ -0,0 +1,53 @@
+version: 2
+
+sphinx:
+  configuration: docs/source/conf.py
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "miniconda-latest"
+  jobs:
+    pre_build:
+      # Download DSPS SSP data and LSST filter curves
+      - mkdir -p docs/source/dsps_drn/filters
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/ssp-data-v1/fsps_v0.4.7_mist_c3k_a_kroupa_wNE_logGasU-2.0_logGasZ0.0.sparse.h5 -P docs/source/dsps_drn
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_u_transmission.h5 -P docs/source/dsps_drn/filters
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_g_transmission.h5 -P docs/source/dsps_drn/filters
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_r_transmission.h5 -P docs/source/dsps_drn/filters
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_i_transmission.h5 -P docs/source/dsps_drn/filters
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_z_transmission.h5 -P docs/source/dsps_drn/filters
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/filters-v1/lsst_y_transmission.h5 -P docs/source/dsps_drn/filters
+      - export DSPS_DRN="dsps_drn"
+
+      # Download a pre-computed example mock for use in demo notebooks
+      - mkdir -p docs/source/mock_download_dir
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/hacc-data-lastjourney-v1/lc_cores-decomposition.txt -P docs/source/mock_download_dir
+
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/mock-galaxies-v1/diffsky_cosmos_260316_05_03_2026_param_collection.hdf5 -P docs/source/mock_download_dir
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/mock-galaxies-v1/diffsky_cosmos_260316_05_03_2026_ssp_data.hdf5 -P docs/source/mock_download_dir
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/mock-galaxies-v1/diffsky_cosmos_260316_05_03_2026_transmission_curves.hdf5 -P docs/source/mock_download_dir
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/mock-galaxies-v1/diffsky_cosmos_260316_05_03_2026_t_table.hdf5 -P docs/source/mock_download_dir
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/mock-galaxies-v1/lc_cores-442.0.diffsky_gals.hdf5 -P docs/source/mock_download_dir
+      - wget -q https://github.com/ArgonneCPAC/diffsky-data/releases/download/mock-galaxies-v1/lc_cores-453.0.diffsky_gals.hdf5 -P docs/source/mock_download_dir
+
+      # # Generate the mock
+      # - export DSPS_DRN="${PWD}/dsps_drn" && python scripts/LJ_LC_MOCKS/make_lj_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
+      # - export DSPS_DRN="${PWD}/dsps_drn" && python scripts/LJ_LC_MOCKS/create_dummy_mock_data.py ci_test_output/dummy_version_name
+
+      # # Copy mock data to where the notebook expects it
+      # - cp ci_test_output/dummy_version_name/* docs/source/mock_download_dir/
+
+      # Use the toolkit to create OpenCosmo-formatted data
+      - mkdir -p docs/source/oc_download_dir
+      - diffpipe run docs/source/mock_download_dir docs/source/oc_download_dir -n 2
+      - cp docs/source/mock_download_dir/diffsky_*.hdf5 docs/source/oc_download_dir/
+      - cp docs/source/mock_download_dir/lc_cores-decomposition.txt docs/source/oc_download_dir/
+
+conda:
+  environment: docs/source/rtd_environment.yaml
+
+python:
+  install:
+    - method: pip
+      path: .

{diffsky-0.3.6 → diffsky-0.3.7}/CHANGES.rst

@@ -1,3 +1,19 @@
+0.3.7 (2026-08-05)
+-------------------
+- Reinstate OpenCosmo docs (https://github.com/ArgonneCPAC/diffsky/pull/439)
+- Migrate top-level modules into subdirectories
+    - phot_utils.py: https://github.com/ArgonneCPAC/diffsky/pull/449
+    - soft_histograms: https://github.com/ArgonneCPAC/diffsky/pull/450
+- Fix bug in `ra, dec`. This bug created a 180 degree offset in RA/phi co-ordinates, which rotated the galaxies away from the dark matter, leading to zero gg-lensing signal (https://github.com/ArgonneCPAC/diffsky/pull/456)
+- Add documentation of Monte Carlo lightcone generators based on diffhalos (https://github.com/ArgonneCPAC/diffsky/pull/458)
+- Ship physical km/s peculiar velocity instead of comoving km/s (https://github.com/ArgonneCPAC/diffsky/pull/464)
+- Remove obsolete prototype calibrations and bring in new models (https://github.com/ArgonneCPAC/diffsky/pull/466)
+- Fix bug in `ra, dec` for synthetic halos (https://github.com/ArgonneCPAC/diffsky/pull/469)
+- Fix bug in ellipsoidal shapes (https://github.com/ArgonneCPAC/diffsky/pull/468)
+- Retune disk axis ratio distribution and size--mass relation (https://github.com/ArgonneCPAC/diffsky/pull/470)
+- Version of code used to produce `c260710_08_02_2026`
+
+
 0.3.6 (2026-06-12)
 -------------------
 - Version of code used to produce cosmos_260316_06_05_2026

{diffsky-0.3.6/diffsky.egg-info → diffsky-0.3.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: diffsky
-Version: 0.3.6
+Version: 0.3.7
 Summary: Library for differentiable generation of synthetic skies
 Author-email: Andrew Hearin <ahearin@anl.gov>
 License: BSD 3-Clause License
@@ -86,10 +86,8 @@ Latest version of diffsky mocks
 
 See `this OpenCosmo tutorial <https://github.com/ArgonneCPAC/opencosmo-examples/blob/main/03-Diffsky/demo_diffmah_diffstar.ipynb/>`_
 for information about how to access the latest mock with OpenCosmo.
-All the publicly available mocks are located at the following path on NERSC::
+The latest release of the mocks is publicly available on NERSC:
 
-    /global/cfs/cdirs/hacc/OpenCosmo/LastJourney/synthetic_galaxies/
+    /global/cfs/cdirs/hacc/OpenCosmo/LastJourney/synthetic_galaxies/c260710_08_02_2026
 
-For the most recent version of the mocks::
-
-    cosmos_260316_05_03_2026 (30 deg^2)
+See  `this PR <https://github.com/ArgonneCPAC/diffsky/pull/472/>`_ for further information about the latest mock.

{diffsky-0.3.6 → diffsky-0.3.7}/README.rst

@@ -36,10 +36,8 @@ Latest version of diffsky mocks
 
 See `this OpenCosmo tutorial <https://github.com/ArgonneCPAC/opencosmo-examples/blob/main/03-Diffsky/demo_diffmah_diffstar.ipynb/>`_
 for information about how to access the latest mock with OpenCosmo.
-All the publicly available mocks are located at the following path on NERSC::
+The latest release of the mocks is publicly available on NERSC:
 
-    /global/cfs/cdirs/hacc/OpenCosmo/LastJourney/synthetic_galaxies/
+    /global/cfs/cdirs/hacc/OpenCosmo/LastJourney/synthetic_galaxies/c260710_08_02_2026
 
-For the most recent version of the mocks::
-
-    cosmos_260316_05_03_2026 (30 deg^2)
+See  `this PR <https://github.com/ArgonneCPAC/diffsky/pull/472/>`_ for further information about the latest mock.

diffsky-0.3.7/diffsky/__init__.py

@@ -0,0 +1,8 @@
+""" """
+
+# flake8: noqa
+
+from ._version import __version__
+from .mass_functions.mc_diffmah_tpeak import mc_subhalos
+from .soft_histograms import diffndhist, diffndhist_lomem, signdhist, signdhist_lomem
+from .utils import phot_utils, tw_utils

diffsky-0.3.7/diffsky/_version.py

@@ -0,0 +1 @@
+__version__ = '0.3.7'

{diffsky-0.3.6 → diffsky-0.3.7}/diffsky/data_loaders/hacc_utils/data_validation/validate_lc_mock.py

@@ -2,17 +2,16 @@
 
 import os
 from glob import glob
-from jax import vmap
+
 import h5py
 import numpy as np
 import yaml
 from dsps.photometry import photometry_kernels as phk
-
+from jax import vmap
 
 from ....param_utils import diffsky_param_wrapper as dpw
 from .. import lc_mock as lcmp
-from .. import sed_from_mock
-from .. import load_flat_hdf5, load_lc_cf, load_lc_mock
+from .. import lightcone_utils, load_flat_hdf5, load_lc_cf, load_lc_mock, sed_from_mock
 
 REQUIRED_METADATA_ATTRS = ("creation_date", "README", "mock_version_name")
 REQUIRED_SOFTWARE_VERSION_INFO = (
@@ -29,7 +28,7 @@ BNPAT_LC_MOCK = "data-{0}.{1}.diffsky_gals.hdf5"
 YAML_REQ_LIST = ("drn_out", "z_min", "z_max")
 HLINE = "----------"
 
-
+BNAME_LC_PATCH_DECOMPOSITION = "lc_cores-decomposition.txt"
 BATCH_SIZE = 50
 
 
@@ -248,6 +247,9 @@ def check_metadata(fn_lc_mock):
         msg.append(s)
         return msg
 
+    _msg = check_lc_cores_decomposition(fn_lc_mock)
+    msg.extend(_msg)
+
     # Check for `index` in metadata
     try:
         assert "index" in all_metadata.keys()
@@ -298,16 +300,8 @@ def check_metadata(fn_lc_mock):
             # Check z_phot_table is reasonable
             z_phot_table = lcmp.load_diffsky_z_phot_table(fn_lc_mock)
             assert z_phot_table.size >= 2
-            # assert np.all(z_phot_table > -1)
-            # assert np.all(z_phot_table < 100)
-
-            # Check has ssp_data
-            # drn_mock = os.path.dirname(fn_lc_mock)
-            # check_has_ssp_data(drn_mock, mock_version_name)
-            # check_has_transmission_curves(drn_mock, mock_version_name)
-
-            # # Check has param_collection
-            # check_has_param_collection(drn_mock, mock_version_name)
+            assert np.all(z_phot_table > -1)
+            assert np.all(z_phot_table < 100)
 
         except:  # noqa
             s = "metadata is incorrect"
@@ -316,6 +310,25 @@ def check_metadata(fn_lc_mock):
     return msg
 
 
+def check_lc_cores_decomposition(fn_lc_mock, bn=BNAME_LC_PATCH_DECOMPOSITION):
+    msg = []
+    drn_mock = os.path.dirname(fn_lc_mock)
+    fn = os.path.join(drn_mock, bn)
+    try:
+        assert os.path.isfile(fn)
+    except AssertionError:
+        s = f"{fn} is missing"
+        msg.append(s)
+
+    try:
+        lightcone_utils.read_lc_ra_dec_patch_decomposition(fn)
+    except:  # noqa
+        s = f"Failure to read {fn} with read_lc_ra_dec_patch_decomposition"
+        msg.append(s)
+
+    return msg
+
+
 def check_host_pos_is_near_galaxy_pos(fn_lc_mock, data=None):
     """host position should be reasonably close to galaxy position"""
     if data is None:

{diffsky-0.3.6 → diffsky-0.3.7}/diffsky/data_loaders/hacc_utils/lc_mock.py

@@ -33,8 +33,8 @@ from ...experimental.black_hole_modeling.black_hole_accretion_rate import (
 )
 from ...experimental.black_hole_modeling.utils import approximate_ssfr_percentile
 from ...experimental.disk_bulge_modeling import disk_bulge_kernels as dbk
-from ...experimental.kernels import dbk_specphot_kernels_merging as dbkspkm
-from ...experimental.kernels import phot_kernels as phkern
+from ...experimental.kernels import dbk_photline_kernels as gd_dbkspkm
+from ...experimental.kernels import phot_kernels_in_situ as gd_phkern
 from ...experimental.size_modeling import smzr_bulge, smzr_disk
 from ...fake_sats import halo_boundary_functions as hbf
 from ...fake_sats import nfw_config_space as nfwcs
@@ -76,7 +76,14 @@ LC_DATA_KEYS_OUT = (
     "lc_patch",
 )
 
-SIZE_KEYS = ("r50_disk", "r50_bulge", "zscore_r50_disk", "zscore_r50_bulge")
+SIZE_KEYS = (
+    "r50_disk_3d",
+    "r50_bulge_3d",
+    "zscore_r50_disk",
+    "zscore_r50_bulge",
+    "r50_disk_2d",
+    "r50_bulge_2d",
+)
 _ORIEN_PATS = (
     "b_over_a_{}",
     "c_over_a_{}",
@@ -338,21 +345,21 @@ def write_batched_lc_sed_mock_to_disk(
 ):
     write_batched_lc_sfh_mock_to_disk(fnout, lc_data, diffsky_data)
 
-    specphot_dict = dict()
+    photline_dict = dict()
     for iband, name in enumerate(filter_nicknames):
-        specphot_dict[name] = phot_info["obs_mags"][:, iband]
+        photline_dict[name] = phot_info["obs_mags"][:, iband]
         if incl_in_situ:
-            specphot_dict[name + "_in_situ"] = phot_info["obs_mags_in_situ"][:, iband]
+            photline_dict[name + "_in_situ"] = phot_info["obs_mags_in_situ"][:, iband]
 
     if incl_in_situ:
-        specphot_dict["logsm_obs_in_situ"] = phot_info["logsm_obs_in_situ"]
+        photline_dict["logsm_obs_in_situ"] = phot_info["logsm_obs_in_situ"]
         assert phot_info["logsm_obs_in_situ"].shape == phot_info["logsm_obs"].shape
 
     for linename in lineflux_nicknames:
-        specphot_dict[linename] = phot_info[linename]
+        photline_dict[linename] = phot_info[linename]
 
     write_batched_mock_data(
-        fnout, specphot_dict, list(specphot_dict.keys()), dataset="data"
+        fnout, photline_dict, list(photline_dict.keys()), dataset="data"
     )
 
     phot_info_colnames = [
@@ -507,7 +514,7 @@ def add_dbk_phot_quantities_to_mock(
     line_wave_table = np.array(ssp_data.ssp_emline_wave)
 
     mc_merge = 1
-    dbk_phot_info, dbk_weights = dbkspkm._mc_dbk_specphot_kern_merging(
+    dbk_phot_info, dbk_weights = gd_dbkspkm._mc_dbk_photline_kern_merging(
         ran_key,
         lc_data["redshift_true"],
         diffsky_data["t_obs"],
@@ -582,11 +589,18 @@ def add_phot_quantities_to_mock(
         [diffsky_data[key] for key in DEFAULT_MAH_PARAMS._fields]
     )
 
-    phot_info, phot_randoms = phkern._mc_phot_kern(
+    upid = np.where(lc_data["central"] == 1, -1, lc_data["top_host_idx_chunk"])
+    lgmu_infall = diffsky_data["logmp_infall"] - diffsky_data["logmhost_infall"]
+    gyr_since_infall = diffsky_data["t_obs"] - diffsky_data["t_infall"]
+    phot_info, phot_randoms, diffstarpop_results = gd_phkern._mc_phot_kern(
         ran_key,
         lc_data["redshift_true"],
         diffsky_data["t_obs"],
         mah_params,
+        upid,
+        lgmu_infall,
+        diffsky_data["logmhost_infall"],
+        gyr_since_infall,
         ssp_data,
         precomputed_ssp_mag_table,
         z_phot_table,
@@ -596,6 +610,7 @@ def add_phot_quantities_to_mock(
         param_collection.spspop_params,
         param_collection.scatter_params,
         param_collection.ssperr_params,
+        param_collection.merging_params,
         sim_info.cosmo_params,
         sim_info.fb,
     )
@@ -629,13 +644,13 @@ def add_morphology_quantities_to_diffsky_data(
         phot_info["logsm_obs"], lc_data["redshift_true"], bulge_size_key
     )
 
-    diffsky_data["r50_disk"] = r50_disk
-    diffsky_data["r50_bulge"] = r50_bulge
+    diffsky_data["r50_disk_3d"] = r50_disk
+    diffsky_data["r50_bulge_3d"] = r50_bulge
     diffsky_data["zscore_r50_disk"] = zscore_disk
     diffsky_data["zscore_r50_bulge"] = zscore_bulge
 
     orientation_key, disk_shape_key, bulge_shape_key = jran.split(morph_key, 3)
-    n = diffsky_data["r50_disk"].size
+    n = diffsky_data["r50_disk_3d"].size
     disk_axis_ratios = disk_shapes.sample_disk_axis_ratios(disk_shape_key, n)
     bulge_axis_ratios = bulge_shapes.sample_bulge_axis_ratios(bulge_shape_key, n)
 
@@ -646,7 +661,14 @@ def add_morphology_quantities_to_diffsky_data(
     diffsky_data["c_over_a_bulge"] = bulge_axis_ratios.c_over_a
 
     ellipse2d_disk, ellipse2d_bulge = mcdbs.mc_disk_bulge_ellipsoids(
-        orientation_key, r50_disk, r50_bulge
+        orientation_key,
+        diffsky_data["r50_disk_3d"],
+        diffsky_data["r50_bulge_3d"],
+        lc_data["x_nfw"],
+        lc_data["y_nfw"],
+        lc_data["z_nfw"],
+        envelop=True,
+        ellipticity_type=0,
     )
 
     diffsky_data["beta_disk"] = ellipse2d_disk.beta
@@ -659,6 +681,13 @@ def add_morphology_quantities_to_diffsky_data(
     diffsky_data["ellipticity_bulge"] = ellipse2d_bulge.ellipticity
     diffsky_data["psi_bulge"] = ellipse2d_bulge.psi
 
+    # Jiachuan Xu:
+    # Assuming a Gaussian profile, the 2D half-light radius would be 0.765*alpha
+    # the 0.765 factor comes from the dimension decrease from 3D to 2D,
+    # where a constant radius encloses more mass in 2D.
+    diffsky_data["r50_disk_2d"] = 0.765 * diffsky_data["alpha_disk"]
+    diffsky_data["r50_bulge_2d"] = 0.765 * diffsky_data["alpha_bulge"]
+
     return diffsky_data
 
 
@@ -677,9 +706,9 @@ def add_black_hole_quantities_to_diffsky_data(lc_data, diffsky_data, phot_info):
 
 def reposition_satellites(sim_info, lc_data, diffsky_data, ran_key, fixed_conc=5.0):
     pos = np.array((lc_data["x"], lc_data["y"], lc_data["z"])).T
-    host_pos = [lc_data[key][lc_data["top_host_idx"]] for key in ("x", "y", "z")]
+    host_pos = [lc_data[key][lc_data["top_host_idx_chunk"]] for key in ("x", "y", "z")]
     host_pos = np.array(host_pos).T
-    host_logmp_obs = diffsky_data["logmp_obs"][lc_data["top_host_idx"]]
+    host_logmp_obs = diffsky_data["logmp_obs"][lc_data["top_host_idx_chunk"]]
 
     diffsky_data["logmp_obs_host"] = host_logmp_obs
     diffsky_data["x_host"] = host_pos[:, 0]

{diffsky-0.3.6 → diffsky-0.3.7}/diffsky/data_loaders/hacc_utils/lightcone_utils.py

@@ -114,7 +114,7 @@ def get_theta_phi(x, y, z):
     rsq = x * x + y * y + z * z
     r = jnp.sqrt(rsq)
     theta = jnp.arccos(z / r)
-    phi = jnp.arctan2(y, x) + jnp.pi
+    phi = jnp.mod(jnp.arctan2(y, x), 2 * jnp.pi)
     return theta, phi
 
 
@@ -149,8 +149,8 @@ def get_xyz_mpc(ra, dec, redshift, cosmo_params):
     )
     theta, phi = get_theta_phi_from_ra_dec(ra, dec)
 
-    x_mpc = r_mpc * jnp.sin(theta) * jnp.cos(phi - jnp.pi)
-    y_mpc = r_mpc * jnp.sin(theta) * jnp.sin(phi - jnp.pi)
+    x_mpc = r_mpc * jnp.sin(theta) * jnp.cos(phi)
+    y_mpc = r_mpc * jnp.sin(theta) * jnp.sin(phi)
     z_mpc = r_mpc * jnp.cos(theta)
 
     return x_mpc, y_mpc, z_mpc