Merge pull request #45 from lowderchris/develop

Merging develop into main

.gitignore

@@ -7,10 +7,19 @@
 *.gcda
 *.gcno
 *.png
+*.pyc
+*.json
 cover_db/
 
 #the local sandbox build
 sandbox/
 
 #any Inline stuff
 _Inline/
+
+#fluxpipe related files
+include/flux/
+blib/
+data/
+local/
+perltidy.ERR

Makefile

@@ -9,7 +9,7 @@ export FL_PREFIX
 
 everything: libbuild install
 
-install: libinstall pdlbuild pdltest pdlinstall
+install: libinstall pdlbuild pdltest pdlinstall install_fluxpipe
 
 libbuild:
 	/bin/sh -c 'cd lib; FL_PREFIX=$(FL_PREFIX) make';
@@ -30,9 +30,15 @@ pdltest:
 pdlinstall:
 	/bin/sh -c 'cd pdl; make install;';
 
+install_fluxpipe:
+	@cd fluxpipe/ && make install_fluxpipe;
+
+uninstall_fluxpipe:
+	@cd fluxpipe/ && make uninstall_fluxpipe;
 
 clean:
 	rm -f *~ \#* ; \
+	rm -f pdl/*.png; \
 	cd lib; \
 	make clean; \
 	cd ..; \
@@ -44,4 +50,10 @@ realclean: clean
 	rm -rf sandbox
 
 uninstall:
-	rm -r $(FL_PREFIX)/lib/libflux.a $(FL_PREFIX)/include/flux ;
+	@echo "\nUninstalling FLUX...";
+	@-rm -rf $(FL_PREFIX)/lib/libflux.a || true;
+	@-rm -rf $(FL_PREFIX)/include/flux || true;
+	@echo "\tFlux uninstall complete.\n";
+
+	@cd fluxpipe/ && make uninstall_fluxpipe;
+

doc/README

@@ -4,3 +4,7 @@ here for a future release.  The original design docs are kept in "old"
 for historical reasons.
 
 -CED 31-Oct-2007
+
+Please see the other files in this directory for some basic documentation.
+The above link is to the wiki, which does not yet contain information about FLUXpipe.
+

doc/mac_install_gilly.md

@@ -0,0 +1,157 @@
+# Macintosh Installation
+
+Here's the path to installing FLUX. Best to run everything as Admin if possible.
+All of these commands should be typed into the terminal.
+If you don't use zsh, you'll need to substitute the shell you use.
+
+## Makefile Installation -----------------------------------
+
+The whole installation process is being integrated into the makefile. See install_flux.sh.
+
+#### 1. If you don't have python installed, get anaconda:
+
+- Download and run the installer from [https://www.anaconda.com/products/individual](https://www.anaconda.com/products/individual)
+
+#### 2. If you don't have perl installed, get perlbrew:
+
+- check ``which perl`` to see if you have perl
+- if not, follow the manual installation instructions under the perl section, below. Don't worry about the cpanminus part.
+
+#### 3. Put the PL and FL_PREFIX paths into /fluxpipe/PREFIX_PATHS.sh
+
+ Examples:
+  ``PL_PATH="/Users/cgilbert/perl5/perlbrew/perls/perl-5.32.0"``
+  ``FL_PATH="/Users/cgilbert/vscode/fluxons/fluxon-mhd"``
+
+#### 4. Build and Run the Makefile
+
+* Go to the fluxpipe directory
+  ``cd fluxon-mhd/fluxpipe``
+* Build the makefile
+  ``perl Makefile.PL``
+* Return to the main directory
+  ``cd ..``
+* Run the top-level make command
+  ``make everything``
+
+Good job! Flux and Fluxpipe should both be working now.
+
+## Manual Installation --------------------------------------
+
+This is already depricated because all of these steps have been moved into the makefile
+
+#### Install Homebrew and Packages: ([https://brew.sh/](https://brew.sh/))) ---------------
+
+- **To get Homebrew, use:**
+  ``% /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"``
+- **Install packages**
+  ``% brew install gnuplot``
+  ``% brew install fftw``
+
+#### Install Perl -------------------------------------------
+
+- **Get perlbrew (recommended, [https://perlbrew.pl/](https://perlbrew.pl/))**
+  ``% \curl -L https://install.perlbrew.pl | bash``
+- **Install the latest version of perl**
+  ``% perlbrew install perl-5.36.1``
+- **Set the system perl to this version**
+  ``% perlbrew switch perl-5.36.1``
+- **Install cpanminus, the perl package manager**
+  ``% curl -L https://cpanmin.us | perl - --sudo App::cpanminus``
+  **~ OR ~**
+  ``% cpan App::cpanminus``
+
+#### Install Python ---------------------------------------
+
+- **If you don't have python installed, start by installing anaconda:**
+
+  - Download the installer from [https://www.anaconda.com/products/individual](https://www.anaconda.com/products/individual)
+  - Run the installer
+- **Prepare the Environment:**
+
+  - initialize conda (once ever)
+    ``% conda init zsh``
+  - restart your terminal (after init)
+    ``% source ~/.zshrc``  ~ OR ~   %``zsh``
+  - make a new environment using conda and activate it
+    ``conda create -n fluxenv``
+    ``conda activate fluxenv``
+    - If you are using an Apple Silicon M1/M2 architecture, please see the footnotes.
+  - navigate to the fluxpipe directory and
+    install the package by running
+    ``pip install -e .``
+
+#### Set the environment variables ---------------------
+
+* **Set the two prefixes**
+  ``export FL_PREFIX='_absolute/_path/_to/fluxon-mhd' ``
+  ``export PL_PREFIX=_absolute/_path/_to/perl ``
+
+  * example: ``export FL_PREFIX=$HOME/vscode/fluxons/fluxon-mhd ``
+    example: ``export PL_PREFIX=/$HOME/perl5/perlbrew/perls/perl-5.32.0 ``
+* **Add them to your environment permanently by running the following commands:**
+  ``echo 'export PL_PREFIX='$PL_PREFIX >> ~/.zshrc ``
+  ``echo 'export FL_PREFIX='$FL_PREFIX >> ~/.zshrc ``
+* **make it so zshenv calls zshrc**
+  ``grep -qF "source ~/.zshrc" ~/.zshenv || echo "source ~/.zshrc" >> ~/.zshenv``
+
+#### Install PDL and other dependencies --------------
+
+- **Install PDL and its dependencies**
+  - Go to Perl directory
+    ``% cd $PL_PREFIX ``
+  - Install PDL
+    ``% cpanm PDL ``
+  - Configure 'local::lib' to set the local build path (leave this as-is).
+    ``% PERL_MM_OPT="INSTALL_BASE=$PL_PREFIX/lib/perl5"``
+    ``% cpanm local::lib ``
+    ``% echo 'eval "$(perl -I$PL_PREFIX/lib/perl5/lib/perl5 -Mlocal::lib=$PL_PREFIX/lib/perl5)"' >> ~/.zshrc ``
+- **Install other dependencies of the project**
+  ``% cpanm File::ShareDir ``
+  ``% cpanm PDL::Graphics::Gnuplot ``
+  ``% cpanm Math::RungeKutta ``
+  and others...
+
+#### Install FLUX -----------------------------------------
+
+- **Get Flux**
+  ``% cd $FL_PREFIX/.. ``
+  ``% git clone https://github.com/lowderchris/fluxon-mhd.git ``
+- **Compile Flux**
+  ``% cd $FL_PREFIX ``
+  ``% sudo make everything ``
+
+### Install FLUXpipe -------------------------------
+
+- Install the fluxpipe pdl package locally
+  ``% cd $FL_PREFIX/fluxpipe ``
+  ``% cpanm --installdeps . ``
+  ``% cpanm --notest --local-lib=local/ .``
+- Set the perl path to the local build and reload the terminal
+  ``echo 'export PERL5LIB=$FL_PREFIX/fluxpipe/local/lib/perl5:$PERL5LIB' >> ~/.zshrc ``
+  ``source ~/.zshrc``
+- - Unfortunately this build must be recompiled after every change. To do this, run
+    ``cd $FL_PREFIX/fluxpipe ``
+    ``cpanm --notest --local-lib=local/ .``
+  - This can be configured to happen automatically in VSCode. You'll need the File Watcher extension.
+    If you place the following lines in your settings.json file in vscode, it will keep your pdl build up to date whenever you save a file.
+
+    ``"filewatcher.commands": [ { "match": ".*\\.(pdl|pm|json)$", "isAsync": true, "event": "onFileChange", "cmd": "cd $FL_PREFIX/fluxpipe && cpanm --notest --local-lib=local/ . && echo $(date) " } ],``
+
+### Footnotes --------------------------------------
+
+[1] Functions to Create Conda Envs for Specific Architectures
+
+**Create x86 conda environment**
+``echo 'conda_create_x86 () { CONDA_SUBDIR=osx-64 conda create -n $@; conda activate $1; }' >> ~/.zshrc``
+
+**Create ARM conda environment**
+``echo 'conda_create_ARM () { CONDA_SUBDIR=osx-arm64 conda create -n $@; conda activate $1; }' >> ~/.zshrc ``
+
+**Run any command with a specified architecture**
+``arch -arm64 <command> <args>``
+
+examples:
+    ``conda_create_ARM myenv_ARM python=3.9``
+    ``conda_create_x86 myenv_x86 python=3.9``
+    ``arch -arm64 brew install qemu``

fluxpipe/.gitignore

@@ -0,0 +1,24 @@
+*~
+\#*
+.DS_Store
+
+#test-coverage-related files & dirs
+*.gcov
+*.gcda
+*.gcno
+*.png
+*.pyc
+*.json
+cover_db/
+
+#the local sandbox build
+sandbox/
+
+#any Inline stuff
+_Inline/
+
+include/flux/
+fluxpipe.egg-info
+blib/
+data/
+local/