ci: use micromamba for builds (#83)

* ci: use micromamba for builds

docs: use mambaforge for builds

* ci: bump versions

.github/workflows/auto-update-files.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: [3.8]
+        python-version: [3.11]
     env:
       OS: ${{ matrix.os }}
       PYTHON: ${{ matrix.python-version }}
@@ -24,17 +24,22 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up conda ${{ matrix.python-version }}
-      uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+    - name: Set up mamba ${{ matrix.python-version }}
+      uses: mamba-org/setup-micromamba@v1
       with:
-        auto-update-conda: true
-        python-version: ${{ matrix.python-version }}
-        activate-environment: icesat2_toolkit
+        micromamba-version: 'latest'
         environment-file: environment.yml
-    - name: Create conda Test Environment
-      run: |
-        conda install flake8 pytest pytest-cov cython
+        init-shell: bash
+        environment-name: icesat2_toolkit
+        cache-environment: true
+        post-cleanup: 'all'
+        create-args: >-
+          python=${{ matrix.python-version }}
+          flake8
+          pytest
+          pytest-cov
+          cython
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -57,7 +62,7 @@ jobs:
         fi
     - name: Create pull request
       if: steps.changes.outputs.DETECTED == 'true'
-      uses: peter-evans/create-pull-request@v3
+      uses: peter-evans/create-pull-request@v5
       with:
         assignees: ${{ github.actor }}
         title: "data: automatic time updates"

.github/workflows/python-publish.yml

@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-20.04
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

.github/workflows/python-request.yml

@@ -22,7 +22,7 @@ jobs:
         shell: bash -l {0}
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up mamba ${{ matrix.python-version }}
       uses: mamba-org/setup-micromamba@v1
       with:

icesat2_toolkit/convert.py

@@ -44,20 +44,15 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     import pandas
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("pandas not available", ImportWarning)
 try:
     import zarr
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("zarr not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 class convert():
     np.seterr(invalid='ignore')

icesat2_toolkit/fit.py

@@ -31,10 +31,7 @@
 try:
     import sklearn.neighbors
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("scikit-learn not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: compress complete list of valid indices into a set of ranges
 def compress_list(i,n):

icesat2_toolkit/io/ATL03.py

@@ -44,10 +44,7 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read ICESat-2 ATL03 HDF5 data files
 def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):

icesat2_toolkit/io/ATL06.py

@@ -42,10 +42,7 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read ICESat-2 ATL06 HDF5 data files
 def read_granule(FILENAME, ATTRIBUTES=False, HISTOGRAM=False,

icesat2_toolkit/io/ATL07.py

@@ -35,10 +35,7 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read ICESat-2 ATL07 HDF5 data files
 def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):

icesat2_toolkit/io/ATL10.py

@@ -30,10 +30,7 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read ICESat-2 ATL10 HDF5 data files
 def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):

icesat2_toolkit/io/ATL11.py

@@ -43,10 +43,7 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read ICESat-2 ATL11 HDF5 data files
 def read_granule(FILENAME, GROUPS=['cycle_stats'], ATTRIBUTES=False,

icesat2_toolkit/io/ATL12.py

@@ -34,10 +34,7 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: read ICESat-2 ATL12 HDF5 data files
 def read_granule(FILENAME, ATTRIBUTES=False, **kwargs):

icesat2_toolkit/spatial.py

@@ -45,20 +45,15 @@
 try:
     import osgeo.gdal, osgeo.osr, osgeo.gdalconst
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("GDAL not available", ImportWarning)
 try:
     import h5py
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     import netCDF4
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("netCDF4 not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 def case_insensitive_filename(filename: str | pathlib.Path):
     """

icesat2_toolkit/tools.py

@@ -28,10 +28,7 @@
     import matplotlib.cm as cm
     import matplotlib.colors as colors
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("matplotlib not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 def from_cpt(filename, use_extremes=True, **kwargs):
     """

icesat2_toolkit/utilities.py

@@ -82,15 +82,11 @@
 try:
     import boto3
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("boto3 not available", ImportWarning)
 try:
     import s3fs
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("s3fs not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: get absolute path within a package from a relative path
 def get_data_path(relpath: list | str | pathlib.Path):

readthedocs.yml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "miniconda3-4.7"
+    python: "mambaforge-22.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

scripts/MPI_DEM_ICESat2_ATL03.py

@@ -115,31 +115,24 @@
 try:
     import fiona
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("fiona not available")
     warnings.warn("Some functions will throw an exception if called")
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     from mpi4py import MPI
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("mpi4py not available", ImportWarning)
 try:
     import osgeo.gdal
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("GDAL not available", ImportWarning)
 try:
     from shapely.geometry import MultiPoint, Polygon
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("shapely not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # digital elevation models
 elevation_dir = {}

scripts/MPI_DEM_ICESat2_ATL06.py

@@ -115,31 +115,24 @@
 try:
     import fiona
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("fiona not available")
     warnings.warn("Some functions will throw an exception if called")
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     from mpi4py import MPI
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("mpi4py not available", ImportWarning)
 try:
     import osgeo.gdal
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("GDAL not available", ImportWarning)
 try:
     from shapely.geometry import MultiPoint, Polygon
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("shapely not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # digital elevation models
 elevation_dir = {}

scripts/MPI_DEM_ICESat2_ATL11.py

@@ -94,31 +94,24 @@
 try:
     import fiona
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("fiona not available")
     warnings.warn("Some functions will throw an exception if called")
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     from mpi4py import MPI
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("mpi4py not available", ImportWarning)
 try:
     import osgeo.gdal
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("GDAL not available", ImportWarning)
 try:
     from shapely.geometry import MultiPoint, Polygon
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("shapely not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # digital elevation models
 elevation_dir = {}

scripts/MPI_ICESat2_ATL03.py

@@ -89,26 +89,20 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     from mpi4py import MPI
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("mpi4py not available", ImportWarning)
 try:
     import sklearn.neighbors
     import sklearn.cluster
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("scikit-learn not available", ImportWarning)
 try:
     import yapc.classify_photons
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("pyYAPC not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: keep track of MPI threads
 def info(rank, size):

scripts/MPI_ICESat2_ATL03_histogram.py

@@ -128,26 +128,20 @@
 try:
     import h5py
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("h5py not available", ImportWarning)
 try:
     from mpi4py import MPI
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("mpi4py not available", ImportWarning)
 try:
     import sklearn.neighbors
     import sklearn.cluster
 except (AttributeError, ImportError, ModuleNotFoundError) as exc:
-    warnings.filterwarnings("module")
     warnings.warn("scikit-learn not available", ImportWarning)
 try:
     import yapc.classify_photons
 except ModuleNotFoundError:
-    warnings.filterwarnings("module")
     warnings.warn("pyYAPC not available", ImportWarning)
-# ignore warnings
-warnings.filterwarnings("ignore")
 
 # PURPOSE: keep track of MPI threads
 def info(rank, size):