release v0.3

.github/workflows/build.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         # mac os 14 at least - runner with Apple Silicon
-        os: [ubuntu-latest, windows-latest, macos-14]
+        os: [ubuntu-latest, windows-latest]  # macos-14, drop mac-os build
     env:
       FC: gfortran
       GCC_V: 12 # only for MACOS
@@ -61,7 +61,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.12"
 
       - name: Install cibuildwheel
         run: pip install cibuildwheel

.gitlab_brgm-ci.yml

@@ -0,0 +1,140 @@
+# Gitlab CI config - Courtesy of T. Janvier (BRGM)
+default:  # linux image on linux runnner
+  image: nexus-docker.brgm.fr/brgm/miniconda3:latest
+  tags:
+    - brgm
+
+.windows: # windows image on windows runnner
+  image: nexus-docker.brgm.fr/brgm/miniconda3:windows
+  tags:
+    - windows-2022-docker
+
+
+stages:
+  - build
+  - test
+  - deploy
+
+
+.version_tag:
+  only: # see https://peps.python.org/pep-0440/
+    variables:
+      - $CI_COMMIT_TAG =~ /^(?P<epoch>\D+)?(?P<version>(?P<release>\d+(?:\.\d+)*)(?P<pre>(?:a|b|rc)\d+?)?((?P<post>\.post\d+))?(?P<dev>\.dev\d+)?(?P<build>\+\S+)?)$/
+  except:
+    - branches
+
+
+# ----- Build ----- #
+
+.build:
+  stage: build
+  extends: .version_tag
+  when: manual
+  script:
+    # build multiple versions using cibuildwheel
+    # - python -m cibuildwheel --output-dir ./dist 
+    # build standalone environment for testing (current package + all dependencies)
+    # - python -m pip wheel -w ./dist/wheelhouse .[test]
+    - python -m pip wheel -w ./dist/ .
+  artifacts:
+    paths:
+    - dist/
+    expose_as: wheel
+    expire_in: 12 hours
+
+
+build-linux:
+  when: manual
+  extends: .build
+  before_script:
+    - echo "gridmarthe ci/cd pipeline"
+    - python --version
+    - mamba install gfortran
+    - gfortran --version
+    - python -m pip install --upgrade pip setuptools wheel
+    - python -m pip install cibuildwheel build
+    # uncomment next line if you need internal dependencies
+    # - python -m pip config set global.index-url ${REGISTRY_NEXUS}/pypi-all/simple
+
+build-windows:
+  when: manual
+  extends: 
+    - .windows
+    - .build
+  before_script:
+    - echo "gridmarthe ci/cd pipeline"
+    - python --version
+    - gfortran --version
+    - pip install --upgrade pip setuptools wheel
+    - pip install cibuildwheel build
+
+
+# ----- Test config ----- #
+
+.test:
+  stage: test
+  extends: .version_tag
+  when: manual
+  script:
+    # - python -c 'import gridmarthe'
+    - pytest tests/
+  # allow_failure: true
+
+
+test-linux:
+  needs: ["build-linux"]
+  extends: .test
+  before_script:
+    - echo "gridmarthe ci/cd pipeline"
+    - python --version
+    - mamba install gfortran
+    - gfortran --version
+    - python -m pip install --no-index --no-deps dist/*none*.whl # no-index: avoid search pypi index ; no-deps, wheels already build
+    - python -m pip install --no-index --no-deps dist/*linux*.whl
+
+
+test-windows:
+  needs: ["build-windows"]
+  extends: 
+    - .windows
+    - .test
+  before_script:
+    - echo "gridmarthe ci/cd pipeline"
+    - python --version
+    - gfortran --version
+    - pip install --no-index --no-deps dist/*none*.whl
+    - pip install --no-index --no-deps dist/*win*.whl
+
+
+
+# ----- Publish ----- #
+
+.deploy:
+  extends: .version_tag
+  stage: deploy
+  except:
+    - branches
+
+
+deploy-nexus_snapshot:
+  needs: ["build-linux", "build-windows"]
+  extends: .deploy
+  before_script:
+    - echo ${NEXUS_URL}
+    - echo ${REGISTRY_NEXUS_USER}
+    - echo ${REGISTRY_NEXUS}
+    - pip install twine
+  script:
+    - twine upload -u ${REGISTRY_NEXUS_USER} -p ${REGISTRY_NEXUS_PASSWORD} --repository-url ${REGISTRY_NEXUS}/pypi-snapshots/ dist/*.whl
+  when: manual
+
+
+deploy-pip:
+  needs: ["build-linux", "build-windows"]
+  extends: .deploy
+  before_script:
+    - pip install twine
+  script:
+    - twine upload --skip-existing --verbose dist/*.whl
+  when: manual
+

Makefile

@@ -4,7 +4,7 @@
 # --------------------------------- #
 #####################################
 #    ONLY FOR LINUX DEVELOP MODE    #
-#        OR CONDA INSTALL           #
+#        OR CONDA SRC INSTALL       #
 #####################################
 
 FC := gfortran
@@ -25,21 +25,25 @@ F90FILES  := lecsem.f90 edsemigl.f90 scan_grid.f90
 #######################
 
 # editable
-# PIPFLAGS ?= --no-build-isolation --editable # meson build version / not functionnal
 PIPFLAGS ?= -e
 #Flags: Warning: flags significantly increase wall-clock and CPU time.
 #Flags are primarily useful for initial check that code compiles correctly
 F2PYOPT =--backend=meson --lower
 
-FFLAGS = -fdefault-real-8
+# These flags are now only used when compiling shared library
+# NOT for install (editable or not): build opt are in meson.build
+FFLAGS = 
+FFLAGS += -fdefault-real-8
 # already O3 in f2py, change it here
-FFLAGS += -O2 
+# FFLAGS += -O2 
 # Position-Independent Code, si shared library, utile
-# FFLAGS +=-fPIC -shared
+FFLAGS +=-fPIC -shared
 FFLAGS += -ffree-line-length-none
-# FFLAGS +=-fallow-argument-mismatch # only gfortran > 12.0
-# FFLAGS += -std=legacy  # not really necessary
-# FFLAGS +=-static # only windows // and not for dev
+# only gfortran > 12.0
+FFLAGS +=-fallow-argument-mismatch
+# legacy is not really necessary ?
+FFLAGS += -std=legacy
+
 
 COMPILE = CC=$(CC) FC=$(FC) FFLAGS="$(FFLAGS)" $(F2PY) -c $(F90FILES) -m lecsem $(F2PYOPT)
 
@@ -49,6 +53,7 @@ COMPILE = CC=$(CC) FC=$(FC) FFLAGS="$(FFLAGS)" $(F2PY) -c $(F90FILES) -m lecsem
 .PHONY: all docs clean requirements wheel
 # all: clean install bakup_pyproj
 all: clean editable
+
 # only compile with f2py for develop purpose
 lib: lecsem.so
 
@@ -78,15 +83,18 @@ lecsem.pyf:
 lecsem.so:
 	cd $(F90SRCDIR); echo "******** Building F2PY Library ********"; \
 	$(COMPILE)
-	# cd $(MAINDIR)
-    # use of `cd` and not $(F90SRCDIR)/lecsem, even if not a good practice in Makefile, 
-    # because meson/f2py does not allow path separator in files.
-	# FC="$(FC)" FFLAGS="$(FFLAGS)" python -m numpy.f2py -c lecsem.pyf lecsem.f90 edsemigl.f90 scan_grid.f90 -m lecsem --backend=meson --lower
-
-# meson editable for test
-editable: requirements
-	$(PY) -m pip install --no-build-isolation --config-settings=editable-verbose=true --editable . -vvv
-    # meson version of editable - for future replacement of setuptools
+
+# use of `cd` and not $(F90SRCDIR)/lecsem, even if not a good practice in Makefile, 
+# because meson/f2py does not allow path separator in files.
+# FC="$(FC)" FFLAGS="$(FFLAGS)" python -m numpy.f2py -c lecsem.pyf lecsem.f90 edsemigl.f90 scan_grid.f90 -m lecsem --backend=meson --lower
+
+# meson editable for dev/testing
+editable: #requirements
+	$(PY) -m pip install --no-build-isolation \
+		--config-settings=editable-verbose=true \
+		--config-settings=setup-args='-Dpip_edit_mode=true' \
+		--editable . \
+		-vvv
 
 wheel:
 	$(PY) -m pip install build

README.md

@@ -24,6 +24,20 @@ The package also install different command line tools: `ncmart` to convert Marth
 
 Full documentation and tutorials can be founded at https://gridmarthe.readthedocs.io
 
+Grids are stored as a 2 dimensions matrix composed of a 1D spatial vector and a time dimension
+(Reduced Horizontal Grid, as recommended for lossless compression by gathering
+in cf-conventions: see [cf-compression-gathering](https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#compression-by-gathering)
+and [cf-reduced-horizontal-grid](https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#reduced-horizontal-grid)).
+This means that the spatial domain is flatten in grid, and each point is associated
+with a index, a x coordinate, a y coordinate, eventually a z coordinate (number of layer
+in most cases), and dx, dy values.
+
+Still, as Marthe meshes are always parallelepiped, the array does *not* necessarily follow the
+[ugrid convention](https://ugrid-conventions.github.io/ugrid-conventions/).
+This may be an evolution for future version if required.
+
+The x, and y coordinates are the center of cell. Dx, Dy are the dimension of the cell.
+
 
 ## Installation
 

changelog.md

@@ -1,19 +1,54 @@
 <!-- gridmarthe changelog -->
 
+v0.3.0
+------
+
+Released on 2025-12-09
+
+* add: beta support for vtk export, based on [vtkwriters](https://gitlab.com/brgm/geomodelling/io/vtkwriters) from ComPass code python ecosystem
+* add: support for reading/plotting velocity field : `gm.read_velocity`, `gm.plot_veloc_quiver`
+* add: beta support for cross section
+* change: attributes in netcdf to be more CF-Conventions compliant:
+    - add crs attributes using `pyrpoj.CRS().to_cf()` for QGIS view compatibilty --> add argument `epsg` in `gm.load_grid_marthe`
+    - add `compress` attribute for zone [https://cfconventions.org](https://cfconventions.org/Data/cf-conventions/cf-conventions-1.11/cf-conventions.html#reduced-horizontal-grid),
+    - fix attributes for coordinates x,y,z / add argument `full_3d` to set z attributes
+    - force attributes for x,y,z to be kept when `gm.assign_coords`
+* add: options to `ncmart` script:
+    - `--dump` (`-H`) to mimic `ncdump -H` command (netcdf CLI tools).
+    - `--attrs` (`-a`) to add global attributes
+    - treat input if already in netcdf fmt (modify it, with scale factor or attrs, to 2D, etc)
+
+
+v0.2.0
+------
+
+<!-- Released on 2025-XX-XX -->
+Unreleased - dev version.
+
+* fix: error when writing grid with time slice (cf. [issue #3](https://gitlab.com/brgm/hydrogeological-modelling/marthe-tools/gridmarthe/-/issues/3))
+* fix: REVERT change from 0.1.3 : zone index is NOT reset (as in 0.1.2 and previous versions).
+    when the `drop_nan` option is used in `load_grid_marthe()`.
+    A new variable 'izone' store the reset form.
+    See [issue #4](https://gitlab.com/brgm/hydrogeological-modelling/marthe-tools/gridmarthe/-/issues/4)
+* change: `nanval` argument in `load_marthe_grid` is rename to `nan_value` as in `write_marthe_grid`
+* change: `keepligcol` argument in `load_marthe_grid` is rename to `add_col_row` to be more coherent with `add_id_grid`
+* change: `xr.Dataset.mart` class accessor is removed. It will be included as wrapper in future marthe python library.
+
+
 v0.1.3
 ------
 
 Released on 2025-09-02
 
-* add geometry functions (get_mask_array, compute_geometry)
+* minor fixes in plot method
+* add geometry functions (`get_mask_array`, `compute_geometry`)
 * add reprojection functions (still experimental)
 * add `martshp` script to easily convert a marthe grid file into a shp/gpkg file in command line
-* code refactoring (lecsem module and global organization)
-* add automatic tests
-* minor fixes in plot method
 * change: rename function to write raster: `to_raster()` instead of `write_raster_from_da()` 
 * change: zone index is reset when the `drop_nan` option is used in `load_grid_marthe()`. A new
   variable 'zone_all' store the old index for the `reset_geometry()` method
+* code refactoring (lecsem module and global organization)
+* add automatic tests
 
 
 v0.1.2

docs/source/_static/custom.css

@@ -1,47 +1,24 @@
 /* Main index page overview cards */
-.sd-card-img-top {
-  width: 33% !important;
-  display: block;
-  margin-left: auto;
-  margin-right: auto;
-  margin-top: 10px;
-}
-
-/* customise nbsphinx ----------------------------------------------- */
-div.nbinput.container div.prompt pre,
-div.nbinput.container div.prompt pre > code {
-  color: var(--pst-color-primary);
-}
-
-div.nboutput.container div.prompt pre,
-div.nboutput.container div.prompt pre > code {
-  color: var(--pst-color-secondary);
-}
-
-div.nbinput.container div.input_area {
-    border: 1px solid var(--pst-color-border);
-}
-
-div.rendered_html table {
-    color: var(--pst-color-text-base);
-}
 
-div.rendered_html thead {
-    border-bottom: 1px solid var(--pst-color-border);
+/* More prominent card borders */ 
+.sd-card {
+  border: 2px solid var(--pst-color-border) !important;
+  border-radius: 3px !important;
 }
 
-div.rendered_html tbody tr:nth-child(odd) {
-    background: var(--pst-color-surface);
+/* fly you fool ! survol */
+.sd-card:hover {
+    border-color: var(--bs-purple) !important;
+    /* sinon voir les couleurs de _static/pydata-sphinx-theme.css à la build */
 }
 
-div.rendered_html tbody tr:hover {
-    background: var(--pst-color-accent-bg);
-}
-
-html[data-theme="dark"] .bd-content .nboutput .output_area.rendered_html {
-    background-color: transparent;
+/* from xarray's doc */
+html[data-theme="dark"] div.cell_output .text_html:has(div.xr-wrap) {
+  background-color: var(--pst-color-on-background) !important;
+  color: var(--pst-color-text-base) !important;
 }
 
+/* Modified from Rameau's doc */
 /* customise footer ------------------------------------------------- */
 .bd-footer .footer-items__end, .bd-footer .footer-items__start {
     gap: 0;
@@ -84,4 +61,4 @@ a.navbar-corporate, a.navbar-corporate:hover {
 /* reduce margin */
 .navbar-nav {
     margin: 0;
-}
+}

docs/source/api/index.rst

@@ -12,5 +12,6 @@ left-hand menu you will find the different categories of the API documentation.
     :maxdepth: 2
 
     io_operations
+    utils_func
     operasem
     plotting

docs/source/api/io_operations.rst

@@ -10,3 +10,5 @@ IO operations
     load_marthe_grid
 
     write_marthe_grid
+
+    read_velocity