Feature ghactions

.github/workflows/ci.yml

@@ -0,0 +1,248 @@
+name: pyemu continuous integration
+
+on: 
+  schedule:
+    - cron: '0 8 * * *' # run at 8 AM UTC (12 am PST)
+  push:
+  pull_request:
+
+jobs:
+  pyemuCI:
+    name: autotests
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [windows-latest, ubuntu-latest, macos-latest] 
+        python-version: [3.8, 3.7, 3.6] # , 3.7, 3.6]
+        run-type: [std]
+        test-path: [
+              "pst_tests_2.py",
+              "utils_tests.py", 
+              "pst_from_tests.py", 
+              "pst_tests.py", 
+              "full_meal_deal_tests.py", 
+              "en_tests.py",
+              "la_tests.py", 
+              "plot_tests.py", 
+              "moouu_tests.py", 
+              "mat_tests.py", 
+              "da_tests.py"
+            ]
+        exclude:
+          - os: macos-latest
+            python-version: 3.7
+          - os: macos-latest
+            python-version: 3.6
+          - os: windows-latest
+            python-version: 3.7
+          - os: windows-latest
+            python-version: 3.6
+        include:
+          - os: ubuntu-latest
+            python-version: 3.8
+            run-type: nb
+            test-path: autotest_notebooks.py
+
+
+    steps:
+    - uses:  actions/checkout@v2.3.4 
+    # - name: Setup Ninja
+      # if: ${{ runner.os == 'Windows' }} 
+    - uses: seanmiddleditch/gha-setup-ninja@master
+
+    - name: Cache Miniconda
+      uses: actions/cache@v2.1.0
+      env:
+        # Increase this value to reset cache if environment.yml has changed
+        CACHE_NUMBER: 0
+      with:
+        path: ~/conda_pkgs_dir
+        key: ${{ runner.os }}-${{ matrix.python-version }}-${{ matrix.run-type }}-${{ env.CACHE_NUMBER }}-${{ hashFiles('etc/environment.yml') }}
+
+    - name: Set Windows ENV
+      if: runner.os == 'Windows'
+      uses: ilammy/msvc-dev-cmd@v1
+
+    # - name: Get specific version CMake, v3.19
+    #   if: ${{ runner.os == 'Windows' }} 
+    #   uses: lukka/get-cmake@latest
+
+    # Standard python fails on windows without GDAL installation
+    # Using custom bash shell ("shell: bash -l {0}") with Miniconda
+    - name: Setup Miniconda
+      uses: conda-incubator/setup-miniconda@v2.0.0
+      with:
+        python-version: ${{ matrix.python-version }}
+        mamba-version: "*"
+        channels: conda-forge
+        auto-update-conda: true
+        activate-environment: pyemu
+        use-only-tar-bz2: true
+
+    - name: Add jupyter and jupytext to notebooks run
+      if: matrix.run-type == 'nb'
+      shell: bash -l {0}
+      run: |
+        mamba install --name pyemu jupyter jupytext
+
+    - name: Add packages to pyemu environment using mamba or conda
+      shell: bash -l {0}
+      run: |
+        if [ "$RUNNER_OS" == "Windows" ]; then
+          conda env update --name pyemu --file etc/environment.yml
+        else
+          mamba env update --name pyemu --file etc/environment.yml
+        fi
+
+    - name: PESTPP exe install
+      shell: bash -l {0}
+      run: |
+        if [[ ! -d "$HOME/.local/bin" ]]; then
+            mkdir -p "$HOME/.local/bin";
+        fi
+        # copy modflow bins to local dir to add to PATH later
+        if [ "$RUNNER_OS" == "Windows" ]; then
+            d="win"
+        elif [ "$RUNNER_OS" == "macOS" ]; then
+            d="mac"
+        elif [ "$RUNNER_OS" == "Linux" ]; then
+            d="linux"
+        else
+            d="unexpectedos"
+            exit 1
+        fi
+        cp -r bin/$d/. "$HOME/.local/bin/"
+        git clone -b develop --depth 1 https://github.com/usgs/pestpp
+        cd pestpp
+        mkdir build && cd build
+        if [[ "$RUNNER_OS" == "Windows" ]]; then
+            cmake -GNinja -DCMAKE_CXX_COMPILER=cl -DCMAKE_C_COMPILER=cl -DCMAKE_BUILD_TYPE=Release ..
+            ninja
+        else
+            cmake -DCMAKE_BUILD_TYPE=Release ..
+            make -j2
+        fi
+        # cd pestpp/src
+        # bindir=../../../../bin/linux COMPILER=gcc CXX=g++ FC=gfortran STATIC=no make -j 20 install
+        cd ..
+        # do we also need to cp to os specific within .local/bin/? probs...
+        find bin -maxdepth 1 -type f -exec cp {} $HOME/.local/bin/. \;
+        # cp -r bin ../bin
+        cd ..
+
+    - name: Install Flopy & pyemu?
+      shell: bash -l {0}
+      run: |
+        git clone -b develop --depth 1 https://github.com/modflowpy/flopy.git
+        cd flopy
+        python setup.py install
+        cd ..
+        pip install https://github.com/modflowpy/pymake/zipball/master
+        python setup.py install
+
+    - name: Add executables directory to path
+      shell: bash
+      run: |
+        echo "$HOME/.local/bin" >> $GITHUB_PATH
+        ls $GITHUB_PATH
+
+    - name: ${{ matrix.test-path }}
+      shell: bash -l {0}
+      run: |
+        nosetests -v --with-id --nocapture --with-timer \
+        --with-coverage --cover-package=pyemu --cover-xml \
+        --cover-xml-file=../coverage.xml -w ./autotest ${{ matrix.test-path }}
+
+
+    # - name: "pst tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest pst_tests.py
+
+    # - name: "utils tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest utils_tests.py
+
+    # - name: "mat tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest mat_tests.py
+
+    # - name: "en tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest en_tests.py
+
+    # - name: "la tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest la_tests.py
+
+    # - name: "PstFrom tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest pst_from_tests.py
+
+    # - name: "da tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest da_tests.py
+
+    # - name: "moouu tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest moouu_tests.py       
+
+    # - name: "full meal deal tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest full_meal_deal_tests.py
+
+    # - name: "plot tests"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest plot_tests.py
+
+    # - name: "pst tests 2"
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest pst_tests_2.py
+
+    # - name: "notebook tests"
+    #   if: ${{ runner.os == 'Linux' && matrix.python-version == '3.8' }}
+    #   shell: bash -l {0}
+    #   run: |
+    #     nosetests -v --with-id --nocapture --with-timer \
+    #     --with-coverage --cover-package=pyemu --cover-xml \
+    #     --cover-xml-file=../coverage.xml -w ./autotest autotest_notebooks.py
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1.0.15
+      with:
+        file: ./coverage.xml
+
+

README.md

@@ -4,11 +4,13 @@ pyEMU
 python modules for model-independent FOSM (first-order, second-moment) (a.k.a linear-based, a.k.a. Bayes linear) uncertainty analyses and data-worth analyses, non-linear uncertainty analyses and interfacing with PEST and PEST++.  pyEMU also has a pure python (pandas and numpy) implementation of ordinary kriging for geostatistical interpolation and support for generating high-dimensional PEST(++) model interfaces, including support for (very) high-dimensional ensemble generation and handling   
 
 Master branch:
+![GA CI Status](https://github.com/pypest/pyemu.svg?branch=master)]
 [![Travis Status](https://travis-ci.org/pypest/pyemu.svg?branch=master)](https://travis-ci.org/pypest/pyemu)
 [![Appveyor Status](https://ci.appveyor.com/api/projects/status/github/pypest/pyemu?branch=master&svg=true)](https://ci.appveyor.com/project/jtwhite79/pyemu)
 [![Coverage Status](https://coveralls.io/repos/github/pypest/pyemu/badge.svg?branch=master)](https://coveralls.io/github/pypest/pyemu?branch=master)
 
 Develop branch:
+![GA CI Status](https://github.com/pypest/pyemu.svg?branch=develop)]
 [![Travis Status](https://travis-ci.org/pypest/pyemu.svg?branch=develop)](https://travis-ci.org/pypest/pyemu)
 [![Appveyor Status](https://ci.appveyor.com/api/projects/status/github/pypest/pyemu?branch=develop&svg=true)](https://ci.appveyor.com/project/jtwhite79/pyemu)
 [![Coverage Status](https://coveralls.io/repos/github/pypest/pyemu/badge.svg?branch=develop)](https://coveralls.io/github/pypest/pyemu?branch=develop)

autotest/full_meal_deal_tests.py

@@ -2,14 +2,22 @@
 import platform
 
 ext = ''
-bin_path = os.path.join("..","..","bin")
-if "linux" in platform.platform().lower():
-    bin_path = os.path.join(bin_path,"linux")
-elif "darwin" in platform.platform().lower() or "macos" in platform.platform().lower():
-    bin_path = os.path.join(bin_path,"mac")
+local_bins = False  # change if wanting to test with local binary exes
+if local_bins:
+    bin_path = os.path.join("..", "..", "bin")
+    if "linux" in platform.platform().lower():
+        pass
+        bin_path = os.path.join(bin_path, "linux")
+    elif "darwin" in platform.platform().lower() or 'macos' in platform.platform().lower():
+        pass
+        bin_path = os.path.join(bin_path, "mac")
+    else:
+        bin_path = os.path.join(bin_path, "win")
+        ext = '.exe'
 else:
-    bin_path = os.path.join(bin_path,"win")
-    ext = '.exe'
+    bin_path = ''
+    if "windows" in platform.platform().lower():
+        ext = '.exe'
 
 
 mf_exe_name = os.path.join(bin_path,"mfnwt")
@@ -32,16 +40,6 @@ def freyberg_test():
         return
     import pyemu
 
-    ext = ''
-    bin_path = os.path.join("..", "..", "bin")
-    if "linux" in platform.platform().lower():
-        bin_path = os.path.join(bin_path, "linux")
-    elif "darwin" in platform.platform().lower() or "macos" in platform.platform().lower():
-        bin_path = os.path.join(bin_path, "mac")
-    else:
-        bin_path = os.path.join(bin_path, "win")
-        ext = '.exe'
-
     org_model_ws = os.path.join("..", "examples", "freyberg_sfr_update")
     nam_file = "freyberg.nam"
     m = flopy.modflow.Modflow.load(nam_file, model_ws=org_model_ws, check=False,forgive=False,
@@ -78,10 +76,10 @@ def freyberg_test():
                                          temporal_bc_props=temp_bc_props,
                                          remove_existing=True,
                                          model_exe_name="mfnwt")
-    tmp = mf_exe_name.split(os.sep)
-    tmp = os.path.join(*tmp[1:])+ext
-    assert os.path.exists(tmp),tmp
-    shutil.copy2(tmp,os.path.join(new_model_ws,"mfnwt"+ext))
+    # tmp = mf_exe_name.split(os.sep)
+    # tmp = os.path.join(*tmp[1:])+ext
+    # assert os.path.exists(tmp),tmp
+    # shutil.copy2(tmp,os.path.join(new_model_ws,"mfnwt"+ext))
     ph.pst.control_data.noptmax = 0
     ph.pst.write(os.path.join(new_model_ws,"test.pst"))
     print("{0} {1}".format(pp_exe_name,"test.pst"), new_model_ws)
@@ -157,16 +155,6 @@ def freyberg_kl_pp_compare():
         return
     import pyemu
 
-    ext = ''
-    bin_path = os.path.join("..", "..", "bin")
-    if "linux" in platform.platform().lower():
-        bin_path = os.path.join(bin_path, "linux")
-    elif "darwin" in platform.platform().lower():
-        bin_path = os.path.join(bin_path, "mac")
-    else:
-        bin_path = os.path.join(bin_path, "win")
-        ext = '.exe'
-
     org_model_ws_base = os.path.join("..", "examples", "freyberg_sfr_update")
     nam_file = "freyberg.nam"
     m = flopy.modflow.Modflow.load(nam_file, model_ws=org_model_ws_base, check=False, forgive=False,
@@ -241,16 +229,6 @@ def freyberg_diff_obs_test():
         return
     import pyemu
 
-    ext = ''
-    bin_path = os.path.join("..", "..", "bin")
-    if "linux" in platform.platform().lower():
-        bin_path = os.path.join(bin_path, "linux")
-    elif "darwin" in platform.platform().lower():
-        bin_path = os.path.join(bin_path, "mac")
-    else:
-        bin_path = os.path.join(bin_path, "win")
-        ext = '.exe'
-
     oorg_model_ws = os.path.join("..", "examples", "freyberg_sfr_update")
     nam_file = "freyberg.nam"
     m = flopy.modflow.Modflow.load(nam_file, model_ws=oorg_model_ws, check=False,forgive=False,
@@ -323,10 +301,10 @@ def freyberg_diff_obs_test():
 
     ph.write_forward_run()
 
-    tmp = mf_exe_name.split(os.sep)
-    tmp = os.path.join(*tmp[1:])+ext
-    assert os.path.exists(tmp),tmp
-    shutil.copy2(tmp,os.path.join(new_model_ws,"mfnwt"+ext))
+    # tmp = mf_exe_name.split(os.sep)
+    # tmp = os.path.join(*tmp[1:])+ext
+    # assert os.path.exists(tmp),tmp
+    # shutil.copy2(tmp,os.path.join(new_model_ws,"mfnwt"+ext))
     ph.pst.control_data.noptmax = 0
     ph.pst.write(os.path.join(new_model_ws,"test.pst"))
     print("{0} {1}".format(pp_exe_name,"test.pst"), new_model_ws)