fix: Update pyproject.yml and add a script for local build (#97)

* Adding script to build all packages

* Update Documentation

* Fix ci

* Missing geos-geomechanics dependency in ci

Author: paloma-martinez

.github/workflows/python-package.yml

@@ -42,6 +42,7 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
         package-name: 
           - geos-ats
+          - geos-geomechanics
           - geos-mesh
           - geos-posp
           - geos-timehistory
@@ -52,8 +53,16 @@ jobs:
           - hdf5-wrapper
           - pygeos-tools
         include:
+          - package-name: geos-geomechanics
+            dependencies: "geos-utils"
+          - package-name: geos-mesh
+            dependencies: "geos-utils geos-geomechanics"
+          - package-name: geos-posp
+            dependencies: "geos-utils geos-mesh geos-geomechanics"
           - package-name: pygeos-tools
             dependencies: "geos-utils geos-mesh"
+          - package-name: geos-timehistory
+            dependencies: "hdf5-wrapper"
     steps:
     - uses: actions/checkout@v4
     - uses: mpi4py/setup-mpi@v1

README.md

@@ -118,7 +118,7 @@ Installation
     python -m venv .venv
     source .venv/bin/activate
     python -m pip install --upgrade pip
-    python -m pip install ./<PACKAGE_NAME>
+    python -m pip install --upgrade ./<PACKAGE_NAME>
     ```
 
     You can test installed package by running the commands:
@@ -129,8 +129,7 @@ Installation
     ```
 
   [!WARNING]
-  Due to local package conflicts with `pip install`, it is recommended either to build the packages one by one, or to inlude only top-level packages (see dependency tree hereabove) in the build list.
-
+   Due to local package conflicts with `pip install`, it is recommended to use the `--upgrade` option when building packages, or to use the script `install_packages.sh` located at the root of the repository.
   [!NOTE]
   geos-pv package cannot be build alone, but together with Paraview ([see Paraview compilation guide](https://gitlab.kitware.com/paraview/paraview/-/blob/master/Documentation/dev/build.md)). It is recommended to use Paraview v5.12+, which is based on python 3.10+. Alternatively, plugins from geos-pv/PVplugins can be manually loaded into Paraview ([see documentation](https://docs.paraview.org/en/latest/ReferenceManual/pythonProgrammableFilter.html#python-algorithm)).
 
@@ -170,12 +169,12 @@ If you want a package to depend on another GEOS Python package (let's say `geos-
 ```
 dependencies = [
     ...
-    "geos-utils @ file:./geos-utils",
+    "geos-utils",
 ]
 ```
 
 [!IMPORTANT]
-geos-pv dependencies are managed using a requirements.txt (together with the setup.py) file where all internal (and external if needed) dependencies are present. It ensures that internal dependency paths are correctly set when plugins are manually loaded into Paraview.
+geos-pv dependencies are managed using a `requirements.txt` (together with the `setup.py`) file where all internal (and external if needed) dependencies are present. It ensures that internal dependency paths are correctly set when plugins are manually loaded into Paraview.
 
 Release
 -------

docs/index.rst

@@ -51,6 +51,8 @@ To do this, you can clone a copy of the geosPythonPackages repository and instal
 .. note::
     To upgrade an existing installation, the python executable in the above command should correspond to the version you indicated in your host config.  If you have previously built the tools, this version will be linked in the build directory: `build_dir/bin/python`.
 
+.. Important::
+    Due to local package dependencies, it is advised to always use the `--upgrade` option when building with the `pip install` option.
 
 Development & Debugging
 ---------------------------

geos-geomechanics/pyproject.toml

@@ -22,7 +22,7 @@ classifiers = [
     "Programming Language :: Python"
 ]
 dependencies=[
-    "geos-utils @ file:./geos-utils",
+    "geos-utils",
     "vtk >= 9.3",
     "numpy >= 2.2",
     "pandas >= 2.2",

geos-posp/pyproject.toml

@@ -34,8 +34,8 @@ keywords = [
 requires-python = ">= 3.10"
 
 dependencies = [
-    "geos-geomechanics @ file:./geos-geomechanics",
-    "geos-utils @ file:./geos-utils",
+    "geos-geomechanics",
+    "geos-utils",
     "vtk >= 9.3",
     "numpy >= 2.2",
     "pandas >= 2.2",

geos-timehistory/pyproject.toml

@@ -21,7 +21,7 @@ dependencies = [
     "matplotlib",
     "h5py",
     "numpy",
-    "hdf5-wrapper @ file:./hdf5-wrapper",
+    "hdf5-wrapper",
 ]
 
 [project.scripts]

install_packages.sh

@@ -0,0 +1,17 @@
+#!/bin/bash
+python -m pip install --upgrade ./geos-utils
+python -m pip install --upgrade ./geos-geomechanics
+python -m pip install --upgrade ./geos-mesh
+python -m pip install --upgrade ./geos-posp
+python -m pip install --upgrade ./geos-xml-tools
+python -m pip install --upgrade ./geos-xml-viewer
+python -m pip install --upgrade ./hdf5-wrapper
+python -m pip install --upgrade ./geos-timehistory
+python -m pip install --upgrade ./pygeos-tools
+python -m pip install --upgrade ./geos-pv
+#! trame install requires npm
+cd ./geos-trame/vue-components
+npm i
+npm run build
+cd ../../
+python -m pip install ./geos-trame