Migrate project management to uv

.github/workflows/ci.yml

@@ -40,130 +40,70 @@ jobs:
     - name: Checkout repo
       uses:  actions/checkout@v5 # checksout this repo
 
-    - name: Set Windows ENV
-      if: runner.os == 'Windows'
-      uses: ilammy/msvc-dev-cmd@v1
-
-    # Setup conda env
-    - name: Install Conda environment using micromamba
-      uses: mamba-org/setup-micromamba@v1
-      with:
-        environment-file: etc/environment.yml
-        environment-name: pyemu
-        create-args: >-
-          python=${{ matrix.python-version }}
-        cache-downloads: true
-        cache-environment: true
-        cache-environment-key: environment-${{ steps.date.outputs.date }}
-        cache-downloads-key: downloads-${{ steps.date.outputs.date }}
-
-    - name: Checkout pypestutils
-      uses:  actions/checkout@v4
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
       with:
-        repository: pypest/pypestutils
-        ref: develop
-        path: pypestutils
-
-#    - name: Install MinGW-w64 tools (Windows)
-#      if: runner.os == 'Windows'
-#      uses: msys2/setup-msys2@v2
-#      with:
-#        msystem: MINGW64
-#        path-type: inherit
-##        install: >-
-##          mingw-w64-x86_64-gcc-fortran
-##          mingw-w64-x86_64-lapack
-##          mingw-w64-x86_64-meson
-##          mingw-w64-x86_64-ninja
-
-    - name: Install meson and gfortran (for ppu)
-      shell: bash -l {0}
-      run: |
-        micromamba install meson gfortran
-
-    - name: Build pypestutils (Windows)
-      if: runner.os == 'Windows'
-      shell: bash -l {0}
-      working-directory: pypestutils
-      env:
-        LDFLAGS: -static-libgcc -static-libgfortran -static-libquadmath -Wl,-Bstatic,--whole-archive -lwinpthread -Wl,--no-whole-archive
-      run: |
-        scripts/build_lib.sh
-
-    - name: Build pypestutils (non-Windows)
-      if: runner.os != 'Windows'
-      shell: bash -l {0}
-      working-directory: pypestutils
-      run: |
-        scripts/build_lib.sh
-
-    - name: Install pypestutils
-      shell: bash -l {0}
-      working-directory: pypestutils
-      run: |
-        pip install -e .
+        python-version: ${{ matrix.python-version }}
 
-    - name: Install pyemu
-      shell: bash -l {0}
+    - name: Install the project
       run: |
-        pip install -e .
-        micromamba list
+        uv sync --locked --extra optional --extra tests
+        uv pip list
 
     - name: Install Modflow executables
       uses: modflowpy/install-modflow-action@v1
 
     - name: Add executables directory to path
+      # need to explicitly use bash shell to get $GITHUB_PATH to work
       shell: bash
       run: |
+        echo "adding bin dir '$MODFLOW_BIN_PATH' to path"
         echo "$MODFLOW_BIN_PATH" >> $GITHUB_PATH
+        echo "adding bin dir '$HOME/.local/bin' to path"
         echo "$HOME/.local/bin" >> $GITHUB_PATH
-        echo $GITHUB_PATH
 
-    # order matters for this step - after setting path to executables
+    # order may matter for this step - after setting path to executables
     - name: Install PEST++ suite using get-pestpp
+      # again think we need bash to get path expansion to work
       shell: bash -l {0}
       run: |
-        get-pestpp --owner pestpp --repo pestpp-nightly-builds :home
+        uv run get-pestpp --owner pestpp --repo pestpp-nightly-builds :home
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-    - name: ${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.test-path }}
+    - name: Verify PEST++ installation
+      shell: bash
+      run: |
+        echo "PATH: $PATH"
+        ls $HOME/.local/bin
+
+    - name: Run tests
+#       For example, using `pytest`
+      # once again need bash (I think) -- windows will run through mingw
       shell: bash -l {0}
       run: |
-        pytest ${{ matrix.test-path }} \
+        uv run pytest ${{ matrix.test-path }} \
         -n=auto \
         -rA -vv --tb=native \
         --durations=20 \
-        --cov=pyemu --cov-report=lcov \
+        --timeout=1200 \
+        --cov=pyemu --cov-report=xml
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Test Notebooks
       if: ${{ matrix.os == 'ubuntu-latest' && matrix.python-version == 3.12 }}
       shell: bash -l {0}
       run: |
-        pytest examples/*.ipynb \
+        uv run pytest examples/*.ipynb \
         -rA -vv --tb=native \
         --nbval-lax --dist loadscope \
-        --cov=pyemu --cov-report=lcov --cov-append
+        --cov=pyemu --cov-report=xml --cov-append
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-    - name: Coveralls
-      uses: coverallsapp/github-action@v2
-      with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        flag-name: ${{ matrix.os }}-${{ matrix.python-version }}-${{ matrix.test-path }}
-        parallel: true
-#        path-to-lcov: autotest/coverage.lcov
-
-  coveralls_finish:
-    needs: pyemuCI
-    runs-on: ubuntu-latest
-    steps:
-    - name: Coveralls Finished
-      uses: coverallsapp/github-action@v2
+    - name: Codecov
+      uses: codecov/codecov-action@v5
       with:
-        github-token: ${{ secrets.GITHUB_TOKEN }}
-        parallel-finished: true
-#        path-to-lcov: autotest/coverage.lcov
+        fail_ci_if_error: true
+        token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/release.yml

@@ -0,0 +1,36 @@
+name: "Publish"
+
+on:
+  push:
+    tags:
+      # Publish on any tag starting with a `v`, e.g., v0.1.0
+      - v*
+
+jobs:
+  run:
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+    permissions:
+      id-token: write
+      contents: read
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v5
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install Python
+        run: uv python install 3.13
+      - name: Build
+        run: uv build
+      # TODO: add some smoke tests here
+#      - name: Smoke test (wheel)
+#        run: uv run --isolated --no-project --with dist/*.whl tests/smoke_test.py
+#      - name: Smoke test (source distribution)
+#        run: uv run --isolated --no-project --with dist/*.tar.gz tests/smoke_test.py
+      - name: Publish
+        run: uv publish
+        # The part below with testpypi only
+        # TODO: remove the next two lines for production usage
+        env:
+          UV_PUBLISH_URL: https://test.pypi.org/legacy/

CITATION.cff

@@ -3,8 +3,8 @@ message: If you use this software, please cite both the article from preferred-c
   and the software itself.
 type: software
 title: pyEMU
-version: 1.4.0
-date-released: '2025-12-8'
+version: 1.4.0.dev3
+date-released: '2025-12-18'
 abstract: A python package for interfacing with PEST and PEST++, and providing model-independent data-worth, and linear and non-linear uncertainty analyses.
 repository-artifact: https://pypi.org/project/pyemu
 repository-code: https://github.com/pypest/pyemu

README.md

@@ -10,10 +10,12 @@ ensemble generation and handling
 Main branch:
 [![pyemu continuous integration](https://github.com/pypest/pyemu/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/pypest/pyemu/actions/workflows/ci.yml)
 [![Coverage Status](https://coveralls.io/repos/github/pypest/pyemu/badge.svg?branch=main)](https://coveralls.io/github/pypest/pyemu?branch=main)
+[![codecov](https://codecov.io/gh/pypest/pyemu/branch/main/graph/badge.svg?token=bnrI1JKvbk)](https://codecov.io/gh/pypest/pyemu)
 
 Develop branch:
 [![pyemu continuous integration](https://github.com/pypest/pyemu/actions/workflows/ci.yml/badge.svg?branch=develop)](https://github.com/pypest/pyemu/actions/workflows/ci.yml)
 [![Coverage Status](https://coveralls.io/repos/github/pypest/pyemu/badge.svg?branch=develop)](https://coveralls.io/github/pypest/pyemu?branch=develop)
+[![codecov](https://codecov.io/gh/pypest/pyemu/graph/badge.svg?token=bnrI1JKvbk)](https://codecov.io/gh/pypest/pyemu)
 
 Documentation
 =============
@@ -104,7 +106,7 @@ pyEMU CI testing, using GitHub actions, has recently been switched over to run w
 We make use of [pytest-xdist](https://pytest-xdist.readthedocs.io/en/latest/) for parallel execution. 
 Some notes that might be helpful for building your PR and testing:
 * Test files are in [./autotest](https://github.com/pypest/pyemu/tree/develop/autotest)
-* Pytest settings are in [./autotest/conftest.py](./autotest/conftest.py) and [./autotest/pytest.ini](./autotest/pytest.ini)
+* Pytest settings are in [./autotest/conftest.py](./autotest/conftest.py) and [./pyproject.toml](autotest/pyproject.toml)
 * Currently, files ending `_tests.py` are collected
 * Functions starting `test_` or ending `_test` are collected
 * ipython notebooks in [./examples](./examples) are also run

autotest/conftest.py

@@ -9,7 +9,6 @@
 collect_ignore = [
     # "emulator_tests.py",
     # "en_tests.py",
-    # "full_meal_deal_tests_2.py",
     # "get_pestpp_tests.py",
     # "la_tests.py",
     # "mat_tests.py",
@@ -18,9 +17,8 @@
     # "plot_tests.py",
     # "pst_from_tests.py",
     # "pst_tests.py",
-    # "pst_tests_2.py",
     # "transformer_tests.py",
-    # "utils_tests.py"
+    # "utils_tests.py",
     # "verf_test.py",
 ]
 
@@ -50,6 +48,7 @@ def get_exe_path(exe_name, forgive=True):
             exe_path = Path(exe_path, "mac")
         else:
             exe_path = Path(exe_path, "win")
+    # if is isn't in bin/<platform> either, give up
     if not (exe_path / exe_name).exists():
         if forgive:
             print(f"Executable {exe_name} not found in {exe_path}, returning None")

autotest/pst_from_tests.py

@@ -76,6 +76,8 @@ def test_freyberg(tmp_path):
     import numpy as np
     import pandas as pd
     from pyemu import PyemuWarning
+    np.show_config()
+
     pd.set_option('display.max_rows', 500)
     pd.set_option('display.max_columns', 500)
     pd.set_option('display.width', 1000)
@@ -295,9 +297,12 @@ def test_freyberg(tmp_path):
     assert np.isclose(pst.phi, 0.), pst.phi
 
 
+@pytest.mark.timeout(method='thread')
 def test_freyberg_prior_build(tmp_path):
     import numpy as np
     import pandas as pd
+    np.show_config()
+
     pd.set_option('display.max_rows', 500)
     pd.set_option('display.max_columns', 500)
     pd.set_option('display.width', 1000)
@@ -2428,7 +2433,7 @@ def mf6_freyberg_varying_idomain(tmp_path):
         print(model_file,sim_val,arr.mean())
 
 
-def xsec_test(tmp_path):
+def test_xsec(tmp_path):
     import numpy as np
     import pandas as pd
     pd.set_option('display.max_rows', 500)
@@ -6249,7 +6254,7 @@ def invest_vertexpp_setup_speed():
     pass
 
 
-def xsec_pars_as_obs_test(tmp_path):
+def test_xsec_pars_as_obs(tmp_path):
     import numpy as np
     import pandas as pd
     pd.set_option('display.max_rows', 500)
@@ -6455,7 +6460,7 @@ def draw_consistency_test(tmp_path):
 
 if __name__ == "__main__":
     draw_consistency_test('.')
-    #xsec_pars_as_obs_test(".")
+    #test_xsec_pars_as_obs(".")
     #add_py_function_test('.')
     #mf6_freyberg_pp_locs_test('.')
     #mf6_subdir_test(".")
@@ -6484,7 +6489,7 @@ def draw_consistency_test(tmp_path):
     #plot_thresh("master_thresh")
     #plot_thresh("master_thresh_mm")
     #mf6_freyberg_varying_idomain()
-    # xsec_test()
+    # test_xsec()
     # mf6_freyberg_short_direct_test()
     # mf6_add_various_obs_test()
     # mf6_subdir_test()