Merge branch 'develop'

.github/workflows/conda_test.yml

@@ -0,0 +1,83 @@
+name: Run tests with miniconda
+on: [push]
+
+jobs:
+  test:
+    name: Miniconda ${{ matrix.os }} Py${{ matrix.pyver }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+        matrix:
+            #os: ["ubuntu-latest", "windows-latest","macos-latest"]
+            os: ["windows-latest","macos-latest"]
+            pyver: ["3.9", "3.10", "3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: test
+          # environment-file: environment.yml
+          python-version: ${{ matrix.pyver }}
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda config --add channels conda-forge
+      - name: Setup environment
+        shell: bash -l {0}
+        run: |
+            git clone --depth 1 -b develop https://github.com/NOAA-ORR-ERD/adios_oil_database.git oil_database
+            conda install -y mamba
+            cd ./py_gnome
+            echo "Setting up conda environment"
+            mamba install -y python=${{ matrix.pyver }}  \
+                             --file conda_requirements.txt \
+                             --file conda_requirements_build.txt \
+                             --file conda_requirements_test.txt \
+                             --file ../oil_database/adios_db/conda_requirements.txt
+      - name: Build Our Packages
+        shell: bash -l {0}
+        run: |
+            pwd
+            ls -la
+            pip install ./oil_database/adios_db/
+            cd ./py_gnome
+            python -m pip install ./
+      - name: Run pytest
+        shell: bash -l {0}
+        run: |
+            cd ./py_gnome/tests/unit_tests
+            pytest --runslow
+      - name: Build wheel file
+        shell: bash -l {0}
+        run: |
+            cd ./py_gnome
+            python -m pip wheel ./
+      - name: Copy files to artifact folder
+        shell: bash -l {0}
+        run: |
+            mkdir installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
+            cp ./py_gnome/*.whl installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
+            cp ./py_gnome/conda_requirements.txt installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v4
+        with: 
+          name: installable-wheel-${{ matrix.os }}-Py${{ matrix.pyver }}
+          path: installable_wheel_${{ matrix.os }}_Py${{ matrix.pyver }}
+
+  lint:
+    name: Flake8 linting
+    runs-on: "ubuntu-latest"
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          activate-environment: lint
+          python-version: 3.9
+          auto-activate-base: false
+      - shell: bash -l {0}
+        run: |
+          conda config --add channels conda-forge
+      - name: Lint
+        shell: bash -l {0}
+        run: |
+            conda install flake8
+            python -m flake8  --exit-zero --statistics py_gnome/gnome/

.gitlab-ci.yml

@@ -5,8 +5,8 @@ variables:
 
 stages:
   - compile
-  - test
   - build
+  - test
 
 cache:
   paths:
@@ -44,22 +44,27 @@ compile_pygnome:
 
     # get the adios_db code: needed for tests and requirements
     - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
+    - cd ./py_gnome
     - conda install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
-                                          --file oil_database/adios_db/conda_requirements.txt
+                                          --file ../oil_database/adios_db/conda_requirements.txt
 
     # install adios_db
-    - pip install oil_database/adios_db/
-
-    - cd ./py_gnome
-    - python setup.py install
-
-    - cd ../  # make sure that it won't find the source gnome package.
-    - python -c "import gnome"  # make sure that it imports
+    - pip install ../oil_database/adios_db/
+
+    # Install pygnome
+    # If you want verbose output including the compiler/linker commands,
+    # run the following command:
+    #   python -m build --no-isolation --config-setting cmake.verbose=true
+    #
+    # And there may be times we want to build a wheel file (.whl)
+    # The following command will build a wheel in the current directory:
+    #   python -m pip wheel ./
+    - python -m pip install ./
 
     # need extra requirements for the docs
     - conda install -y --file conda_requirements_docs.txt
-    - cd py_gnome/documentation && make html  # build the docs
+    - cd documentation && make html  # build the docs
   artifacts:
     when: always
     expire_in: 15 days
@@ -76,8 +81,10 @@ test_pygnome:
   allow_failure: false
   image: registry.orr.noaa.gov/erd/centos-conda/$IMAGE_NAME$PYTHON_VER
   script:
-    - conda install -y --file conda_requirements_test.txt
+    - conda install -y --file py_gnome/conda_requirements_test.txt
     - cd ./py_gnome/tests/unit_tests && pytest --runslow
+
+    # save the package list if tests pass
     - conda list > conda_packages.txt
 
 # Ideally, all the scripts in "testing_scripts" should run without errors,
@@ -109,56 +116,78 @@ test_pygnome_windows:
     - windows
     - visual-studio-22
   allow_failure: true
+  cache: []
   before_script:
+    - echo $CI_PIPELINE_ID
+
+    # where are we?
     - Get-Location
-    - dir
+    - Get-ChildItem | % { $_.FullName }  # this should list the current folder
+    - $Env:PathOrig = $Env:Path
+    - $Env:CurrDir = Get-Location
+
+    # Where is our conda installation?
+    # This will tell us where python is installed.  This could change periodically
+    #- Get-ChildItem -Path 'C:\Python310' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+    #- Get-ChildItem -Path 'C:\ProgramData\miniforge3' -Recurse -Include "python.exe", "conda.exe" | % { $_.FullName }
+
     # make sure conda is on the path first in the path
-    - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path
-    - $Env:Path = 'C:\ProgramData\Miniconda3\;' + $Env:Path
-    - $Env:Path = 'C:\ProgramData\Miniconda3\Scripts;' + $Env:Path
+    - $Env:Path = 'C:\ProgramData\miniforge3\;' +
+                  'C:\ProgramData\miniforge3\Scripts;' +
+                  'C:\ProgramData\miniforge3\Lib\bin;' +
+                  $Env:PathOrig
+    - $Env:Path -split ';'
 
-    - echo "Our environemt vars:"
-    - $Env:Path
+    - python -c "import sys; print(sys.executable)"
+
+    # This might be changing our current directory.  It only needs to be run
+    # one time anyway, so we will comment it out.
+    #- Invoke-Expression "conda shell.powershell hook"
+    #- conda init powershell
+
+    # On SO, it was suggested that this would perform a `conda init`
+    # without needing to restart PowerShell.  So we will test it.
+    - C:\ProgramData\miniforge3\shell\condabin\conda-hook.ps1
 
-    - echo $CI_PIPELINE_ID
-    - conda activate ./$CI_PIPELINE_ID
     - conda config --add channels defaults
     - conda config --add channels conda-forge
     - conda config --get channels
     - conda config --set channel_priority strict
-  script:
-    - echo "Building and testing PyGNOME"
-
-    # # make sure our conda package is first in the path
-    # - $Env:Path = 'C:\ProgramData\Miniconda3\Library\bin;' + $Env:Path
-    # - $Env:Path = 'C:\ProgramData\Miniconda3\;' + $Env:Path
-    # - $Env:Path = 'C:\ProgramData\Miniconda3\Scripts;' + $Env:Path
 
-    - echo "Our environemt vars:"
-    - $Env:Path
+    - conda create -y -p ./pygnome python=$PYTHON_VER
 
-    - echo "Python is running from:"
-    - python -c "import sys; print(sys.executable)"
+    #- $Env:Path = '' +
+    #              (Get-Location) + '\pygnome\;' +
+    #              (Get-Location) + '\pygnome\Scripts\;' +
+    #              (Get-Location) + '\pygnome\Lib\bin\;' +
+    #              $Env:PathOrig
+    - conda activate ./pygnome
+  script:
+    - echo "Building and testing PyGNOME"
 
     # get the adios_db code: needed for tests and requirements
     - git clone --depth 1 -b develop https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.orr.noaa.gov/gnome/oil_database/oil_database.git
 
     - conda install -y python=$PYTHON_VER mamba
+    - cd ./py_gnome
     - echo "Setting up conda environment"
     - mamba install -y python=$PYTHON_VER --file conda_requirements.txt
                                           --file conda_requirements_build.txt
                                           --file conda_requirements_test.txt
-                                          --file oil_database/adios_db/conda_requirements.txt
+                                          --file ../oil_database/adios_db/conda_requirements.txt
 
-    - echo "Building PyGNOME"
-    - cd ./py_gnome
-    # - python setup.py install
-    - python setup.py develop
-
-    # Make sure that it imports from some folder other than the
-    # gnome package folder.
-    # - cd ../
-    # - python -c "import gnome"
+    # install adios_db
+    - pip install ../oil_database/adios_db/
+
+    # Install pygnome
+    # If you want verbose output including the compiler/linker commands,
+    # run the following command:
+    #   python -m build --no-isolation --config-setting cmake.verbose=true
+    #
+    # And there may be times we want to build a wheel file (.whl)
+    # The following command will build a wheel in the current directory:
+    #   python -m pip wheel ./
+    - python -m pip install ./
 
     - cd ./tests/unit_tests
     - pytest --runslow
@@ -180,9 +209,9 @@ build_develop:
 
     # build the py_gnome image
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-    - docker build . --build-arg PYTHON_VER=$PYTHON_VER -t registry.orr.noaa.gov/gnome/pygnome:develop
+    - docker build . --build-arg PYTHON_VER=$PYTHON_VER -t registry.orr.noaa.gov/gnome/pygnome:$CI_COMMIT_BRANCH
     - docker login -u $CI_REGISTRY_USER -p $CI_REGISTRY_PASSWORD $CI_REGISTRY
-    - docker push registry.orr.noaa.gov/gnome/pygnome:develop
+    - docker push registry.orr.noaa.gov/gnome/pygnome:$CI_COMMIT_BRANCH
 
 build_main:
   stage: build

Install_without_conda.rst

@@ -28,7 +28,7 @@ Building everything by hand / with pip
 
 It is always good practice to create and run a complex system like this in a virtual environment of some sort: virtualenv, pipenv, etc.
 
-A virtual environment is **not required** to run PyGNOME.
+A virtual environment is *not required* to run PyGNOME.
 But you may be working in an environment (on a corporate network, for example) that restricts your access to the system files on your computer.
 In such a case, you may require a virtualenv in order to freely install python packages in python's site-packages dir. (site-packages is the standard place where python installers will put packages after building them)
 
@@ -121,18 +121,14 @@ Download and install the newest Windows executable distribution of
 
 `Python 3.10 <http://www.python.org/download/>`_
 
-(3.9 -- 3.11 shoule work)
+(3.9 -- 3.12 should work)
 
 A number of the packages that GNOME depends on have very complex and
 brittle build processes, and depend on third-party libraries that can be
 a challenge to build.
 
 Fortunately, many of them are available as binary wheels on PyPi
 
-Another option is to use a Python scientific distribution, such as
-`Anaconda <https://www.anaconda.com/products/distribution>`_ -- in which case, stop and read the ``Installing.rst`` file.
-
-
 Dependencies can be installed using the command::
 
     > pip install -r requirements.txt
@@ -152,25 +148,17 @@ Build PyGNOME
     > cd PyGNOME/py_gnome
     > pip install -r requirements.txt
 
-3. Install the adios_db pacakge -- it is under active development along  with py_gnome, so it's best to install that from source as well:
+3. Install the adios_db package -- it is under active development along  with py_gnome, so it's best to install that from source as well:
 
    https://github.com/NOAA-ORR-ERD/adios_oil_database/tree/production/adios_db
 
-4. build the ``py_gnome`` module in develop or install mode:
+4. build the ``py_gnome`` module in editable or install mode.
 
-   ``> python setup.py build``
+   ``> python -m pip install ./``
 
    or
 
-   ``> python setup.py install``
-
-   or
-
-   ``> python setup.py develop``
-
-The other option you may need is ``cleanall``, which should clean the development environment -- good to do after puling new code from git::
-
-   > python setup.py cleanall
+   ``> python -m pip install --editable ./``
 
 
 5. If this successfully completes, then run the unit tests::