diffsky 0.3.4__tar.gz → 0.3.5__tar.gz

{diffsky-0.3.4 → diffsky-0.3.5}/.github/workflows/linting.yaml

@@ -1,4 +1,4 @@
-name: Flake8 test of source code
+name: Flake8 source code
 
 on:
   push:
@@ -14,7 +14,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
           python-version: 3.11
           channels: conda-forge,defaults

diffsky-0.3.5/.github/workflows/mockgen_opencosmo_main.yaml

@@ -0,0 +1,143 @@
+name: make_lj_mock.py synthetic halos (opencosmo main)
+
+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 make_lj_mock.py testing_lj_mock_config.yaml
+    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@v4
+        with:
+          python-version: 3.12
+          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>=7 \
+            h5py \
+            mpi4py \
+            mpich \
+            pytest \
+            opencosmo
+          conda uninstall diffmah --force
+          conda uninstall diffstar --force
+          conda uninstall dsps --force
+          conda uninstall diffhalos --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
+          pip install --no-deps --no-build-isolation git+https://github.com/ArgonneCPAC/diffhalos.git
+
+          pip install git+https://github.com/ArgonneCPAC/opencosmo.git
+          pip install git+https://github.com/AstroPatty/diffpipe.git
+
+          python -m pip install --no-build-isolation --no-deps -e .
+
+      - name: download dsps data
+        shell: bash -l {0}
+        run: |
+          # Create data directory
+          mkdir -p dsps_drn/filters
+
+          # Download data
+          cd dsps_drn
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_emlines.sparse.hdf5
+          wget 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
+
+          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
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_r_transmission.h5
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_i_transmission.h5
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_z_transmission.h5
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/filters/lsst_y_transmission.h5
+          cd ..
+          cd ..
+
+          # Set environment variable
+          export DSPS_DRN="${GITHUB_WORKSPACE}/dsps_drn"
+          echo "DSPS_DRN=${DSPS_DRN}" >> $GITHUB_ENV
+
+      - 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_lj_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
+
+      - name: verify script completed
+        shell: bash -l {0}
+        run: |
+          echo "make_lj_mock.py ran successfully for testing_lj_mock_config.yaml"
+
+      - name: validate mock
+        shell: bash -l {0}
+        run: |
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/dummy_version_name
+
+      # - name: Create dummy diffsky galaxies for OpenCosmo
+      #   shell: bash -l {0}
+      #   run: |
+      #     python scripts/LJ_LC_MOCKS/create_dummy_mock_data.py ci_test_output/dummy_version_name
+
+      # - name: OpenCosmo toolkit data conversion
+      #   shell: bash -l {0}
+      #   run: |
+      #     mkdir -p ci_test_output/oc_dummy_version_name
+      #     cp ci_test_output/dummy_version_name/* ci_test_output/oc_dummy_version_name/
+      #     rm -rf ci_test_output/oc_dummy_version_name/lc_cores*.hdf5
+      #     diffpipe run ci_test_output/dummy_version_name ci_test_output/oc_dummy_version_name -n 2
+
+      # - name: Run tests on OpenCosmo-formatted data
+      #   shell: bash -l {0}
+      #   run: |
+      #     echo "ci_test_output/oc_dummy_version_name ready for testing"
+      #     # Here we can execute a testing script of ci_test_output/oc_dummy_version_name
+      #     export RUN_OPENCOSMO_TESTS="true"
+      #     export OPENCOSMO_DIFFSKY_DATA_PATH="ci_test_output/oc_dummy_version_name"
+      #     pytest diffsky/data_loaders/opencosmo_utils/test
+
+      - name: remove cosmos_fit mock
+        shell: bash -l {0}
+        run: |
+          rm -rf ci_test_output

diffsky-0.3.4/.github/workflows/mock_generation_test.yaml → diffsky-0.3.5/.github/workflows/mockgen_opencosmo_release.yaml

@@ -1,4 +1,4 @@
-name: Test mock-production script runs with synthetic halos
+name: make_lj_mock.py synthetic halos (opencosmo latest)
 
 on:
   workflow_dispatch: null
@@ -12,7 +12,7 @@ on:
 
 jobs:
   mock-generation:
-    name: python make_ou26_mock.py -synthetic_cores 1
+    name: python make_lj_mock.py testing_lj_mock_config.yaml
     runs-on: "ubuntu-latest"
 
     steps:
@@ -28,9 +28,9 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
           channels: conda-forge
           channel-priority: strict
           show-channel-urls: true
@@ -51,18 +51,41 @@ jobs:
             setuptools \
             "setuptools_scm>=7,<8" \
             matplotlib \
-            astropy \
+            astropy>=7 \
             h5py \
             mpi4py \
-            mpich
+            mpich \
+            pytest \
+            opencosmo
+          conda install hdf5plugin=5.0
           conda uninstall diffmah --force
           conda uninstall diffstar --force
           conda uninstall dsps --force
+          conda uninstall diffhalos --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
+          pip install --no-deps --no-build-isolation git+https://github.com/ArgonneCPAC/diffhalos.git
+
+          pip install git+https://github.com/AstroPatty/diffpipe.git
+
           python -m pip install --no-build-isolation --no-deps -e .
 
+      - name: check opencosmo version
+        shell: bash -l {0}
+        env:
+          GH_TOKEN: ${{ secrets.CPAC_PRIVATE_REPO_TOKEN }}
+        run: |
+          OPENCOSMO_CURRENT_VERSION=$(gh release view --repo ArgonneCPAC/OpenCosmo --json tagName --jq .tagName)
+          OPENCOSMO_INSTALLED_VERSION=$(conda list opencosmo | awk 'NR==4 {print $2}')
+          if [[ "$OPENCOSMO_CURRENT_VERSION" != "$OPENCOSMO_INSTALLED_VERSION" ]]; then
+            echo "Error: installed opencosmo ${OPENCOSMO_LATEST_VERSION} but latest version is ${OPENCOSMO_CURRENT_VERSION}"
+            exit 1
+          else
+            echo "Successfully installed opencosmo ${OPENCOSMO_LATEST_VERSION}"
+          fi
+
+
       - name: download dsps data
         shell: bash -l {0}
         run: |
@@ -71,7 +94,8 @@ jobs:
 
           # Download data
           cd dsps_drn
-          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_emlines.hdf5
+          wget https://portal.nersc.gov/project/hacc/aphearin/DSPS_data/ssp_data_fsps_v3.2_emlines.sparse.hdf5
+          wget 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
           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
@@ -86,42 +110,6 @@ jobs:
           export DSPS_DRN="${GITHUB_WORKSPACE}/dsps_drn"
           echo "DSPS_DRN=${DSPS_DRN}" >> $GITHUB_ENV
 
-      - 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_batch.py \
-            poboy \
-            0.01 \
-            0.2 \
-            0 \
-            1 \
-            ci_test_output \
-            ci_test_mock \
-            -sfh_model smdpl_dr1 \
-            -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/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: |
@@ -129,65 +117,38 @@ jobs:
           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
+          mpiexec -n 1 python scripts/LJ_LC_MOCKS/make_lj_mock.py scripts/LJ_LC_MOCKS/testing_lj_mock_config.yaml
 
       - name: verify script completed
         shell: bash -l {0}
         run: |
-          echo "sfh_model mock generated successfully"
+          echo "make_lj_mock.py ran successfully for testing_lj_mock_config.yaml"
 
       - 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
+          python scripts/LJ_LC_MOCKS/inspect_lc_mock.py ci_test_output/dummy_version_name
+
+      # - name: Create dummy diffsky galaxies for OpenCosmo
+      #   shell: bash -l {0}
+      #   run: |
+      #     python scripts/LJ_LC_MOCKS/create_dummy_mock_data.py ci_test_output/dummy_version_name
+
+      # - name: OpenCosmo toolkit data conversion
+      #   shell: bash -l {0}
+      #   run: |
+      #     mkdir -p ci_test_output/oc_dummy_version_name
+      #     cp ci_test_output/dummy_version_name/* ci_test_output/oc_dummy_version_name/
+      #     rm -rf ci_test_output/oc_dummy_version_name/lc_cores*.hdf5
+      #     diffpipe run ci_test_output/dummy_version_name ci_test_output/oc_dummy_version_name -n 2
+
+      # - name: Run tests on OpenCosmo-formatted data
+      #   shell: bash -l {0}
+      #   run: |
+      #     export RUN_OPENCOSMO_TESTS="true"
+      #     export OPENCOSMO_DIFFSKY_DATA_PATH="ci_test_output/oc_dummy_version_name"
+      #     pytest diffsky/data_loaders/opencosmo_utils/test
 
-      - 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}

{diffsky-0.3.4 → diffsky-0.3.5}/.github/workflows/monthly-warning-test.yaml

@@ -1,4 +1,4 @@
-name: Monthly test for warnings in diffstuff main branches
+name: Monthly test for warnings
 
 on:
   workflow_dispatch: null
@@ -16,9 +16,9 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
           channels: conda-forge,defaults
           channel-priority: strict
           show-channel-urls: true
@@ -46,16 +46,22 @@ jobs:
             setuptools \
             "setuptools_scm>=7,<8" \
             matplotlib \
-            astropy \
             python-build
           pip uninstall diffmah --yes
           pip uninstall diffstar --yes
           pip uninstall dsps --yes
+          pip uninstall diffhalos --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
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffhalos.git
           python -m pip install --no-build-isolation --no-deps -e .
 
+      - name: check numpy version
+        shell: bash -l {0}
+        run: |
+          python -c "import numpy; print(numpy.__version__)"
+
       - name: test that no warnings are raised
         shell: bash -l {0}
         run: |

{diffsky-0.3.4 → diffsky-0.3.5}/.github/workflows/shape_optimization.yaml

@@ -1,4 +1,4 @@
-name: Test script for optimizing galaxy shapes
+name: script optimizing galaxy shapes
 
 on:
   workflow_dispatch: null
@@ -28,9 +28,9 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
           channels: conda-forge
           channel-priority: strict
           show-channel-urls: true
@@ -51,7 +51,6 @@ jobs:
             setuptools \
             "setuptools_scm>=7,<8" \
             matplotlib \
-            astropy \
             h5py \
             mpi4py \
             mpich
@@ -63,6 +62,11 @@ jobs:
           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: check numpy version
+        shell: bash -l {0}
+        run: |
+          python -c "import numpy; print(numpy.__version__)"
+
       - name: run disk optimization script
         shell: bash -l {0}
         run: |

{diffsky-0.3.4 → diffsky-0.3.5}/.github/workflows/test_latest_releases.yaml

@@ -1,4 +1,4 @@
-name: Test against latest diffstuff releases
+name: pytest latest diffstuff
 
 on:
   push:
@@ -16,9 +16,9 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
           channels: conda-forge,defaults
           channel-priority: strict
           show-channel-urls: true
@@ -45,17 +45,22 @@ jobs:
             setuptools \
             "setuptools_scm>=7,<8" \
             matplotlib \
-            astropy \
             python-build
+          pip install git+https://github.com/ArgonneCPAC/diffhalos.git
           python -m pip install --no-build-isolation --no-deps -e .
 
+      - name: check numpy version
+        shell: bash -l {0}
+        run: |
+          python -c "import numpy; print(numpy.__version__)"
+
       - name: test
         shell: bash -l {0}
         run: |
           pytest -v diffsky --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 

{diffsky-0.3.4 → diffsky-0.3.5}/.github/workflows/test_main_branch.yaml

@@ -1,4 +1,4 @@
-name: Test with Main Branch Dependencies
+name: pytest latest diffstuff
 
 on:
   push:
@@ -16,9 +16,9 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: conda-incubator/setup-miniconda@v3
+      - uses: conda-incubator/setup-miniconda@v4
         with:
-          python-version: 3.11
+          python-version: 3.12
           channels: conda-forge,defaults
           channel-priority: strict
           show-channel-urls: true
@@ -46,23 +46,29 @@ jobs:
             "setuptools_scm>=7,<8" \
             matplotlib \
             scipy \
-            astropy \
             python-build
           pip uninstall diffmah --yes
           pip uninstall diffstar --yes
           pip uninstall dsps --yes
+          pip uninstall diffhalos --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
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffhalos.git
           python -m pip install --no-build-isolation --no-deps -e .
 
+      - name: check numpy version
+        shell: bash -l {0}
+        run: |
+          python -c "import numpy; print(numpy.__version__)"
+
       - name: test
         shell: bash -l {0}
         run: |
           pytest -v diffsky --cov --cov-report=xml
 
       - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v6
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 

diffsky-0.3.5/.github/workflows/test_main_branch_no_extra_deps.yaml

@@ -0,0 +1,100 @@
+name: weekly pytest latest diffstuff no extra deps
+
+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: pytest with diffmah/diffstar/dsps@main
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v6
+        with:
+          fetch-depth: 0
+
+      - uses: conda-incubator/setup-miniconda@v4
+        with:
+          python-version: 3.12
+          channels: conda-forge,defaults
+          channel-priority: strict
+          show-channel-urls: true
+          miniforge-version: latest
+
+      - name: configure conda and install code
+      # Test against current main branch of all diff+ dependencies
+        shell: bash -l {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.CPAC_PRIVATE_REPO_TOKEN }}
+          GITHUB_USER: ${{ secrets.GH_USR_TESTING_TOKEN }}
+
+      # Test against conda-forge for all dependencies except use main branch for dsps
+        run: |
+          conda config --set always_yes yes
+          conda install --quiet \
+            --file=requirements.txt
+          conda install -y -q \
+            flake8 \
+            pytest \
+            pytest-xdist \
+            pytest-cov \
+            pip \
+            setuptools \
+            "setuptools_scm>=7,<8" \
+            python-build
+          pip uninstall diffmah --yes
+          pip uninstall diffstar --yes
+          pip uninstall dsps --yes
+          pip uninstall diffhalos --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
+          pip install --no-deps git+https://github.com/ArgonneCPAC/diffhalos.git
+          python -m pip install --no-build-isolation --no-deps -e .
+
+      - name: check numpy version
+        shell: bash -l {0}
+        run: |
+          python -c "import numpy; print(numpy.__version__)"
+
+      - name: test
+        shell: bash -l {0}
+        run: |
+          pytest -v diffsky --cov --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v6
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+
+      - 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 .