Fixes in docs and HDF5 support (#497)

* Fixes in docs and HDF5 support

- Fixed issue #495
- Enabled HDF5 supported build and fixed HDF5 linking issue
- Updated installation instructions, README.
- Updated packaging to upload wheels only on master branch

* Fix for mesonbuild/meson#13985

Fixes build issue on Ubuntu

* Raise exception in `connect` and `element` when failed

- The shell only generates an error message when an attempt to connect
two objects via message fails. This caused hard to debug errors. Now
the wrapper function raises RuntimeError in such case.

- `element(path)` returned the roor element when `path` does not
exist, again causing hard to find bugs. This now raises RuntimeError.

* Minor fix in installation instructions

* Updated moose.element() to raise error for nonexistent path

* Implemented HHChannelF and HHGateF for formula based evaluation

- Refactored HHChannelBase and created a class hierarchy for HHGate
- Added test scripts for HHChannelF (`test_hhchannelf.py`) and updated test
for HHChannel (`test_hhchannel.py`)
- Moved voltage clamp code for test fixture into `tests/core/ephys.py`
- Removed old `Func` class from default scheduling

Author: subhacom

.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.