deploy v0.4

.editorconfig

@@ -0,0 +1,21 @@
+# EditorConfig is awesome: https://editorconfig.org
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+charset = utf-8
+
+[Makefile]
+indent_style = tab
+
+[*.yml,*.yaml]
+indent_style = space
+indent_size = 2

.gitignore

@@ -3,8 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
+# C/F90 extensions
 *.so
+*.o
 *.mod
 *.pyd
 *.dll
@@ -114,8 +115,6 @@ celerybeat.pid
 env/
 venv/
 ENV/
-env.bak/
-venv.bak/
 .venvrc
 
 # Spyder project settings
@@ -145,7 +144,11 @@ cython_debug/
 # vscodes
 .vscode
 
-
 *.bak
+*.out
 dev/
-*.out
+test-read
+Cal_river_network.listing
+
+.benchmarks/
+

.readthedocs.yaml

@@ -3,9 +3,9 @@
 version: 2
 
 build:
-  os: "ubuntu-22.04"
+  os: "ubuntu-24.04"
   tools:
-    python: "3.10"
+    python: "3.12"
   apt_packages:
     - gcc
     - gfortran
@@ -15,17 +15,8 @@ build:
   jobs:
     pre_build:
       - pip install numpy charset_normalizer meson meson-python
-      #- cd src/gridmarthe/lecsem ; CC=gcc FC=gfortran f2py -c lecsem.f90 edsemigl.f90 scan_grid.f90 -m lecsem --backend=meson --lower
-      - pip install .[gis,doc]
+      - pip install .[opt,doc]
       - python3 -c "import gridmarthe"
 
-# python:
-  # install:
-    # - method: pip
-      # path: .
-      # extra_requirements: 
-        # - gis
-        # - doc
-
 sphinx:
-  configuration: docs/source/conf.py
+  configuration: docs/source/conf.py

Makefile

@@ -4,7 +4,6 @@
 # --------------------------------- #
 #####################################
 #    ONLY FOR LINUX DEVELOP MODE    #
-#        OR CONDA SRC INSTALL       #
 #####################################
 
 FC := gfortran
@@ -20,61 +19,63 @@ F2PY = $(PY) -m numpy.f2py
 
 ###### SOURCES ########
 MAINDIR := $(shell pwd)
-F90SRCDIR := $(MAINDIR)/src/gridmarthe/lecsem
-F90FILES  := lecsem.f90 edsemigl.f90 scan_grid.f90
+F90SRCDIR := $(MAINDIR)/src/gridmarthe/core
+
+F90FILES  := $(F90SRCDIR)/lecsem/lecsem.f90 \
+			 $(F90SRCDIR)/lecsem/edsemigl.f90 \
+             $(F90SRCDIR)/utils/xy_dxdy.f90 \
+			 $(F90SRCDIR)/flowdirect/analy_topo.f90 \
+			 $(F90SRCDIR)/flowdirect/calc_direct_drainage.f90 \
+			 $(F90SRCDIR)/flowdirect/num_8_voisins.f90 \
+			 $(F90SRCDIR)/rivernetwork/Cal_reseau_hydro.f90 \
+			 $(F90SRCDIR)/rivernetwork/Convert_Direct_Drain.f90 \
+			 $(F90SRCDIR)/rivernetwork/Definit_Sous_Bassins.f90 \
+			 $(F90SRCDIR)/rivernetwork/Dir_Drain_LigCol_Ava.f90 \
+			 $(F90SRCDIR)/rivernetwork/Direct_Drain_Mai_Ava.f90 \
+			 $(F90SRCDIR)/rivernetwork/Mai_Ava_Strahl_Surf_Drai.f90 \
+			 $(F90SRCDIR)/rivernetwork/Mai_Exu_Surf_Drai.f90 \
+			 $(F90SRCDIR)/rivernetwork/Verif_Surf_Stat_Hydro.f90 \
+			 $(F90SRCDIR)/dessin/colle_segments.f90 \
+			 $(F90SRCDIR)/modgridmarthe.f90
 #######################
 
-# editable
-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
 
-# These flags are now only used when compiling shared library
+# These flags are now only used when compiling shared library for testing
 # NOT for install (editable or not): build opt are in meson.build
-FFLAGS = 
+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
+# FFLAGS += -shared  # => bug
 FFLAGS += -ffree-line-length-none
-# only gfortran > 12.0
+# 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)
+# legacy is not really necessary
+# FFLAGS += -std=legacy
 
+COMPILE = CC=$(CC) FC=$(FC) FFLAGS="$(FFLAGS)" $(F2PY) -c $(F90FILES) -m coremod $(F2PYOPT)
 
 # ------------- Rules ------------- #
 
-.PHONY: all docs clean requirements wheel
-# all: clean install bakup_pyproj
+.PHONY: all doc clean requirements editable meson wheel sdist
 all: clean editable
 
 # only compile with f2py for develop purpose
 lib: lecsem.so
 
-
 doc:
 	cd docs; $(MAKE) html
 
-# deprecated
-# setuptools: pyproject.toml
-# 	cp pyproject.toml pyproject.bak ; sed -i '16s/# //' pyproject.toml ; sed -i '17s/^/# /' pyproject.toml
-#     # change to setuptools for editable version
-# 
-# bakup_pyproj: pyproject.toml
-# 	mv pyproject.bak pyproject.toml
-#     # format pyproject.{toml,bak} non accepté par make ?
-
 requirements:
-	$(PY) -m pip install charset_normalizer numpy meson meson-python
+	$(PY) -m pip install charset_normalizer numpy meson meson-python pytest
 
-#install: requirements lecsem.so setuptools bakup_pyproj
-#	$(PY) -m pip install $(PIPFLAGS) . -vvv
+conda-req:
+	mamba install charset-normalizer numpy meson meson-python pytest h5netcdf xarray pandas geopandas
 
 lecsem.pyf:
 	cd $(F90SRCDIR); echo "******** Generating signature ********"; \
@@ -83,19 +84,22 @@ lecsem.pyf:
 lecsem.so:
 	cd $(F90SRCDIR); echo "******** Building F2PY Library ********"; \
 	$(COMPILE)
-	
-# use of `cd` and not $(F90SRCDIR)/lecsem, even if not a good practice in Makefile, 
+
+# 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 \
+editable:
+	$(PY) -m pip install --no-build-isolation --no-deps \
 		--config-settings=editable-verbose=true \
 		--config-settings=setup-args='-Dpip_edit_mode=true' \
 		--editable . \
 		-vvv
 
+meson:
+	rm -rf build/ ; meson setup build; cd build; meson compile
+
 wheel:
 	$(PY) -m pip install build
 	$(PY) -m build -w
@@ -108,4 +112,3 @@ clean:
 	cd $(F90SRCDIR); \
 	rm -f *.so *.o *.mod *.c *pywrappers* *.dll *.pyd ; \
 	cd $(MAINDIR)
-

README.md

@@ -36,39 +36,36 @@ Still, as Marthe meshes are always parallelepiped, the array does *not* necessar
 [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.
+The `x`, and `y` coordinates are the center of cell. `dx`, `dy` are the dimensions of the cell.
 
 
 ## Installation
 
 ### From pip
 
 
-On pip, `gridmarthe` is available for GNU/Linux, macOS and Windows for python >=3.10.
+On pip, `gridmarthe` is available for GNU/Linux, and Windows for python >=3.10.
 Users can install it with:
 
 ```bash
 pip install gridmarthe
+# or with all optional dependencies
+pip install gridmarthe[opt]
 ```
 
-For GNU/Linux and MacOS, the package needs gfotran/gcc to run.
-
-Linux, example with debian/ubuntu:
+For UNIX systems, the package needs gfortran/gcc shared libraries to run.
+For example, using a Debian-based GNU/Linux distribution, one can install
+gcc with:
 
 ```bash
 sudo apt install gcc gfortran
 ```
 
 
-MacOS:
-
-```bash
-brew install gcc gfortran
-```
-
 ### From conda-forge
 
-`gridmarthe` is also available in the `conda-forge` channel. Conda users can install it with:
+`gridmarthe` is also available in the `conda-forge` channel (Linux, Windows).
+Conda users can install it with:
 
 ```bash
 conda install gridmarthe
@@ -79,8 +76,8 @@ mamba install gridmarthe
 
 ### From sources
 
-`gridmarthe` use some Fortran modules which need
-to be compiled before local installation.
+`gridmarthe` use some Fortran modules which need to be compiled before local installation,
+hence user/developer who want to install from sources will need a Fortran and a C compiler.
 
 #### Compilation and installation
 
@@ -93,49 +90,54 @@ cd gridmarthe
 
 ##### With pip (Unix-like OS)
 
-On a Unix-like machine, with gfortran, ninja-build, python3, the project `Makefile` will compile Fortran sources and install
-**in development mode** the package.
+On a Unix-like machine, with gfortran, ninja-build, python3, the project `Makefile` will compile
+Fortran sources and install **in development mode** (i.e. **with** editable flag) the package.
 
 ```bash
+make requirements
 make
 ```
 
-or, without the development mode :
+or, *without* the development/editable mode :
 
 ```bash
 pip install .
 ```
 
-On a windows machine, it is possible to compile with gfortran
-(mingw project https://mingw-w64.org/ or https://winlibs.com/#download-release ; or `choco install mingw`).
-Neverless, the simpliest way is to use a conda environment (miniforge with mambalib is recommended) to install gcc/gfortran,
-and install the project.
+On a Windows machine, it is possible to compile with gfortran/gcc
+(mingw project https://mingw-w64.org/ or https://winlibs.com/#download-release ;
+it can also be installed with chocolatey `choco install mingw`, or with conda
+with conda-forge packages `mingw-w64`, `gcc` and `gfortran`).
+
 
 ##### With conda (recommended on Windows)
 
-It is also possible to install gridmarthe in a conda environment. An environment file is provided (example with mamba):
+It is also possible to install gridmarthe in a conda environment.
+An environment file is provided (example with mamba):
 
 ```bash
 mamba env create -n gm -f environment.yml
 mamba activate gm
-pip install --no-deps .
+make
 ```
 
-Here, the development mode is *not* available (yet, with the meson build).
-One can add the `-e` flag in pip command, or use `conda-build`:
+This will install the library using pip editable mode, but with dependencies
+installed from conda-forge.
+
+Alternatively, you can use `conda-build`:
 
 ```bash
 mamba env create -n gm -f environment.yml
 mamba activate gm
 mamba install conda-build
-make lib
+make lib  # only compile shared library for python bindings
 conda develop src/
 ```
 
 
 ## Usage
 
-Simple examples can be found in the 
+Simple examples can be found in the
 [documentation](https://gridmarthe.readthedocs.io/en/stable/user_guide/index.html).
 
 
@@ -147,7 +149,15 @@ This program is free software and released under the terms of the
 
 ## Authors and acknowledgment
 
-A. Manlay and J.P. Vergnes, (c) BRGM
+gridmarthe is released by (C) BRGM, French Geological Survey
+
+Authors and contributors:
+
+- A. Manlay,
+- J.P. Vergnes,
+- S. Wang,
+- S. Lopez,
+- S. Magne
 
 
 ## References