Fixes in docs and HDF5 support

.github/workflows/package.yml

@@ -8,7 +8,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-14, windows-latest]
+        os: [ubuntu-latest, macos-14, macos-15, windows-latest]
         build_type: [Release]
         c_compiler: [clang]
         python-version: ['3.11']
@@ -105,6 +105,7 @@ jobs:
           python -m cibuildwheel --output-dir wheelhouse
           dir wheelhouse
       - name: Upload packages
+        if: github.ref == 'refs/heads/main'
         uses: xresloader/upload-to-github-release@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

INSTALL.md

@@ -43,9 +43,9 @@ To build `MOOSE` from source, you need `meson`, `ninja`, `pkg-config`, and `pyth
 recommend to use Python 3.9 or higher.  To build and install with `pip`, you also need `meson-python`.
 
 For platform specific instructions, see:
-- Linux: UbuntuBuild.md
-- MacOSX: AppleM1Build.md
-- Windows: WindowsBuild.md
+- Linux: [UbuntuBuild.md](UbuntuBuild.md)
+- MacOSX: [AppleM1Build.md](AppleM1Build.md)
+- Windows: [WindowsBuild.md](WindowsBuild.md)
 
 Briefly,
 1. Build environment: make sure that the following packages are installed on your system.
@@ -68,6 +68,14 @@ Briefly,
 $ pip install git+https://github.com/BhallaLab/moose-core --user
 ```
 
+This will install the `master` branch of MOOSE. If you want a specific fork/branch, modify the address:
+
+```
+$ pip install git+https://github.com/subhacom/moose-core@fix495merge --user
+```
+
+will install the fix495merge branch from `subhacom`'s fork of `moose-core`.
+
 ## Post installation
 
 You can check that moose is installed and initializes correctly by running:

README.md

@@ -41,7 +41,7 @@ https://github.com/BhallaLab/moose-examples.
 # Build 
 
 To build `pymoose`, follow instructions given in
-[INSTALLATION.md](INSTALLATION.md) and for platform specific
+[INSTALL.md](INSTALL.md) and for platform specific
 information see:
 - Linux: [UbuntuBuild.md](UbuntuBuild.md)
 - MacOSX: [AppleM1Build.md](AppleM1Build.md)

UbuntuBuild.md

@@ -47,7 +47,7 @@ conda activate moose
 cd moose-core
 
 meson setup --wipe _build --prefix=`pwd`/_build_install -Duse_mpi=false -Dbuildtype=release
-ninja -v -C _build 
+meson compile -v -C _build 
 meson install -C _build
 ```
 

WindowsBuild.md

@@ -53,8 +53,8 @@ $env:PATH="$env:PATH;C:\Program Files\LLVM\bin"
 
 ```
 cd moose-core
-meson setup --wipe _build -Duse_mpi=false --buildtype=release
-ninja -v -C _build 
+meson setup --wipe _build -Duse_mpi=false --buildtype=release --vsenv
+meson compile -vC _build 
 meson install -C _build
 ```
 *Note: If you want to keep the installation in local folder replace the third command with: `meson setup --wipe _build --prefix={absolute-path} -Duse_mpi=false --buildtype=release` where `absolute-path` is the full path of the folder you want to install it in. You will have to add the `Lib\site-packages` directory within this to your PATH environment variable to make `moose` module visible to Python.*
@@ -68,7 +68,7 @@ Meson provides many builtin options: https://mesonbuild.com/Builtin-options.html
 
 
 	```
-	meson setup --wipe _build --prefix=%CD%\\_build_install -Duse_mpi=false -Dbuildtype=debug
+	meson setup --wipe _build --prefix=%CD%\\_build_install -Duse_mpi=false -Dbuildtype=debug  --vsenv
 	```
 
 	You can either use `buildtype` option alone or use the two options `debug` and `optimization` for finer grained control over the build. According to `meson` documentation `-Dbuildtype=debug` will create a debug build with optimization level 0 (i.e., no optimization, passing `-O0 -g` to GCC), `-Dbuildtype=debugoptimized`  will create a debug build with optimization level 2 (equivalent to `-Ddebug=true -Doptimization=2`), `-Dbuildtype=release` will create a release build with optimization level 3 (equivalent to `-Ddebug=false -Doptimization=3`), and `-Dbuildtype=minsize` will create a release build with space optimization (passing `-Os` to GCC).
@@ -91,7 +91,7 @@ is to make a copy of `python3x.lib` named `python3x_d.lib` in the same
 directory (`libs`). After that, you can run meson setup as follows:
 
 ```
-meson setup --wipe _build --prefix=%CD%\\_build_install -Duse_mpi=false --buildtype=debug
+meson setup --wipe _build --prefix=%CD%\\_build_install -Duse_mpi=false --buildtype=debug --vsenv
 ```
 
 and then go through the rest of the steps.