Merge pull request #2 from jhmatthews/docs-patch

Docs patch

.github/workflows/build.yml

@@ -1,4 +1,4 @@
-name: "Python: continuous integration tests"
+name: "Sirocco: continuous integration tests"
 on:
   push:
     branches:
@@ -9,69 +9,69 @@ on:
       - "dev"
       - "main"
 env:
-  PYTHON: ${{ github.workspace }}
+  SIROCCO: ${{ github.workspace }}
 jobs:
   greeting:
     name: Greeting job
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: "Print out environment variables"
       run: |
         echo "WORKSPACE IS $GITHUB_WORKSPACE"
-        echo "PYTHON ENV VARIABLE IS: $PYTHON"
+        echo "SIROCCO ENV VARIABLE IS: $SIROCCO"
 
   build_and_test:
-    name: Build Python and run tests
+    name: Build Sirocco and run tests
     runs-on: ubuntu-latest
     needs: greeting
     steps:
     - uses: actions/checkout@v3
     #- name: "Installing build dependencies"
     #  run: sudo apt update && apt install -y build-essential cmake
 
-    - name: Configuring Python
+    - name: Configuring Sirocco
       run: ./configure
-    - name: Build GH Workflow version of Python
+    - name: Build GH Workflow version of Sirocco
       run: make gh_workflow_install
 
     - uses: actions/setup-python@v3
       with:
         python-version: '3.x' # Version range
-    - name: Install Python (the language) dependencies
+    - name: Install python dependencies
       run: |
         python -m pip install --upgrade pip
         pip install wheel
-        cd $PYTHON/examples/gh-workflow/
+        cd $SIROCCO/examples/gh-workflow/
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
 
 #    - name: Compile programs, again
 #      run: |
-#        cd $PYTHON/source
+#        cd $SIROCCO/source
 #        make CC=gcc INDENT=no all
 
-    - name: Checking Python compiled and can read in inputs correctly
+    - name: Checking Sirocco compiled and can read in inputs correctly
       run: |
-        cd $PYTHON/examples/gh-workflow/
-        $PYTHON/bin/Setup_Py_Dir
-        $PYTHON/bin/py -i cv_macro_benchmark
-        $PYTHON/bin/py -i cv_standard
-        $PYTHON/bin/py -i fiducial_agn
-        $PYTHON/bin/py -i 1d_sn
-        $PYTHON/bin/py -i -d sv_detailedmode
-        $PYTHON/bin/py -i agn_ss_2010_modela
-        $PYTHON/bin/py -i XRB_standard.pf
-        $PYTHON/bin/py -i ngc5548
-        $PYTHON/bin/py -i lamp_post
-        $PYTHON/bin/py -i cv_standard_import
+        cd $SIROCCO/examples/gh-workflow/
+        $SIROCCO/bin/Setup_Py_Dir
+        $SIROCCO/bin/sirocco -i cv_macro_benchmark
+        $SIROCCO/bin/sirocco -i cv_standard
+        $SIROCCO/bin/sirocco -i fiducial_agn
+        $SIROCCO/bin/sirocco -i 1d_sn
+        $SIROCCO/bin/sirocco -i -d sv_detailedmode
+        $SIROCCO/bin/sirocco -i agn_ss_2010_modela
+        $SIROCCO/bin/sirocco -i XRB_standard.pf
+        $SIROCCO/bin/sirocco -i ngc5548
+        $SIROCCO/bin/sirocco -i lamp_post
+        $SIROCCO/bin/sirocco -i cv_standard_import
 
     - name: Running unit tests
       run: |
-        cd $PYTHON/source/tests
+        cd $SIROCCO/source/tests
         make check CC=gcc
 
     - name: Running Balmer test case
       run: |
-        cd $PYTHON/examples/gh-workflow/
-        $PYTHON/bin/py -f -v 1 balmer_test
-        python $PYTHON/py_progs/balmer_decrement.py balmer_test
+        cd $SIROCCO/examples/gh-workflow/
+        $SIROCCO/bin/sirocco -f -v 1 balmer_test
+        python $SIROCCO/py_progs/balmer_decrement.py balmer_test

Makefile.in

@@ -1,26 +1,26 @@
 #
-# This is the Makefile for the python related programs
+# This is the Makefile for the Sirocco related programs
 #
-# Make sure you have defined $PYTHON as this directory first
+# Make sure you have defined $SIROCCO as this directory first
 # then type:
 #
 #   ./configure [--with-cuda]
 # 	make install
 #
-# If this fails, consult https://github.com/agnwinds/python/wiki/Installing-Python
+# If this fails, consult documentation
 # for manual install.
 
 CMAKE = mpicc
-GSL_LOCATION = $(PYTHON)/software/gsl-2.6
-CUNIT_LOCATION = $(PYTHON)/software/cunit-3.2.7
+GSL_LOCATION = $(SIROCCO)/software/gsl-2.6
+CUNIT_LOCATION = $(SIROCCO)/software/cunit-3.2.7
 INSTALL_LIBS = True
 
 ifeq (True, $(INSTALL_LIBS))
 	# GNU Science library -- math routines
 	MOVE_GSL = \
-		mkdir $(PYTHON)/include/gsl; \
-		mv $(GSL_LOCATION)/include/gsl/* $(PYTHON)/include/gsl; \
-		mv $(GSL_LOCATION)/lib/lib* $(PYTHON)/lib;
+		mkdir $(SIROCCO)/include/gsl; \
+		mv $(GSL_LOCATION)/include/gsl/* $(SIROCCO)/include/gsl; \
+		mv $(GSL_LOCATION)/lib/lib* $(SIROCCO)/lib;
 	INSTALL_GSL = \
 		cd $(GSL_LOCATION); \
 		./configure --disable-shared --prefix=$(GSL_LOCATION) cc=gcc CPP=cpp; \
@@ -40,19 +40,19 @@ ifeq (True, $(INSTALL_LIBS))
 	# CUnit -- unit test framework: built using CMake, so only build if installed
 	ifneq ($(shell which cmake), )
 		INSTALL_CUNIT = \
-			mkdir -p $(PYTHON)/include/CUnit; \
+			mkdir -p $(SIROCCO)/include/CUnit; \
 			cd $(CUNIT_LOCATION); \
 			mkdir -p build; \
 			cd build; \
 			cmake ..; \
 			cmake --build .; \
-			mv CUnit/libcunit.a $(PYTHON)/lib; \
-			cp ../CUnit/CUnit/*.h $(PYTHON)/include/CUnit/; \
+			mv CUnit/libcunit.a $(SIROCCO)/lib; \
+			cp ../CUnit/CUnit/*.h $(SIROCCO)/include/CUnit/; \
 			cd ..; \
 			rm -rf build;
 
 		MAKE_CHECK = \
-			cd $(PYTHON)/source; \
+			cd $(SIROCCO)/source; \
 			make check CC=$(CMAKE)
 	else
 		INSTALL_CUNIT = echo 'Unable to install CUnit as CMake (https://cmake.org) is not installed'
@@ -65,14 +65,14 @@ else
 	MAKE_CHECK =
 endif
 
-MAKE_PYTHON = \
-	cd $(PYTHON)/source; \
+MAKE_SIROCCO = \
+	cd $(SIROCCO)/source; \
 	make CC=$(CMAKE) INDENT=no all \
 
-# Compile and install the libraries and Python
+# Compile and install the libraries and Sirocco
 install:
-	@echo 'Installing Python. the radiative transfer code'
-	@echo 'Installing in directory '$(PYTHON)
+	@echo 'Installing Sirocco. the radiative transfer code'
+	@echo 'Installing in directory '$(SIROCCO)
 
 	# Then make GSL library
 	@echo 'Installing GSL library...'
@@ -84,13 +84,13 @@ install:
 
 	# Finally, make the latest release
 	@echo 'Making source code...'
-	$(MAKE_PYTHON)
+	$(MAKE_SIROCCO)
 	@echo 'all done'
 
-# Install Python for travis -- as above, minus post-installation checks for GSL
+# Install Sirocco for travis -- as above, minus post-installation checks for GSL
 gh_workflow_install:
-	@echo 'Installing Python. the radiative transfer code'
-	@echo 'Installing in directory '$(PYTHON)
+	@echo 'Installing Sirocco. the radiative transfer code'
+	@echo 'Installing in directory '$(SIROCCO)
 
 	# Then make GSL library
 	@echo 'Installing GSL library...'
@@ -102,12 +102,12 @@ gh_workflow_install:
 
 	#finally, make the latest release
 	@echo 'Making source code...'
-	$(MAKE_PYTHON)
+	$(MAKE_SIROCCO)
 	@echo 'all done'
 
-# Runs Python's unit tests
+# Runs Sirocco's unit tests
 check:
-	cd $(PYTHON)/source; make check
+	cd $(SIROCCO)/source; make check
 
 # Runs through the install for GSL and post-installation checks
 gsl:
@@ -119,24 +119,24 @@ cunit:
 	@echo 'Installing CUnit unit test framework'
 	$(INSTALL_CUNIT)
 
-# Run the regular clean for the libraries and Python. CUnit doesn't need this,
+# Run the regular clean for the libraries and Sirocco. CUnit doesn't need this,
 # as we delete the CMake build directory after installing it
 clean:
 	rm -f *.o *~
 	cd $(GSL_LOCATION); make clean;
 	rm -rf $(CUNIT_LOCATION)/build
-	cd $(PYTHON)/source/; make clean
+	cd $(SIROCCO)/source/; make clean
 
-# Runs a more rigorous clean for the libraries and Python. CUnit doesn't need
+# Runs a more rigorous clean for the libraries and Sirocco. CUnit doesn't need
 # this, as we delete the CMake build directory after installing it
 distclean:
 	rm -f *.o *~
 	cd $(GSL_LOCATION); make distclean
 	rm -rf $(CUNIT_LOCATION)/build
-	cd $(PYTHON)/source/; make clean
+	cd $(SIROCCO)/source/; make clean
 
 # Remove just the libraries
 rm_lib:
-	rm -rf $(PYTHON)/include/gsl
-	rm -rf $(PYTHON)/include/CUnit
-	rm -f $(PYTHON)/lib/lib*
+	rm -rf $(SIROCCO)/include/gsl
+	rm -rf $(SIROCCO)/include/CUnit
+	rm -f $(SIROCCO)/lib/lib*

README.md

@@ -2,21 +2,22 @@
 
 *Sirocco* (Simulating Ionization and Radiation in Outflows Created by Compact Objects) is a Monte Carlo radiative transfer code which uses the Sobolev approximation. The code was formerly known as Python and renamed in October 2024. It has been developed by Knox Long, Christian Knigge, Stuart Sim, Nick Higginbottom, James Matthews, Sam Manghamm Edward Parkinson, Mandy Hewitt and Nico Scepi. The code has been used for a variety of research projects invovling the winds of cataclysmic variables, young stellar objects, X-ray binaries and AGN.
 
-The code is under active development, but we are looking for beta users to test the code, and potentially use it for their own research. If you are interested in using Sirocco please contact Knox Long via long[at]stsci[dot]edu. 
+The code is under active development, but we are looking for beta users to test the code, and potentially use it for their own research. If you are interested in using Sirocco please contact Knox Long via long[at]stsci[dot]edu 
+or James Matthews via james[dot]matthews[at]physics[dot]ox[dot]ac[dot]uk.
 
-Documentation is hosted on [ReadTheDocs](http://agnwinds.readthedocs.io/en/dev/).
+Documentation is hosted on [ReadTheDocs](http://sirocco-rt.readthedocs.io/en/dev/).
 
 ## CI \& Docs Build Status
 
-[![C/C++ CI](https://github.com/agnwinds/python/actions/workflows/build.yml/badge.svg)](https://github.com/agnwinds/python/actions/workflows/build.yml)
+[![C/C++ CI](https://github.com/sirocco-rt/sirocco/actions/workflows/build.yml/badge.svg)](https://github.com/sirocco-rt/sirocco/actions/workflows/build.yml)
 
-[![Documentation Status](https://readthedocs.org/projects/agnwinds/badge/?version=latest)](https://agnwinds.readthedocs.io/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/sirocco-rt/badge/?version=latest)](https://sirocco-rt.readthedocs.io/en/latest/?badge=latest)
 
 ## Installation
 
 Sirocco and the various routines associated are set up in a self-contained directory structure. The basic directory structure and the data files that one needs to run Sirocco need to be retrieved and compiled. 
 
-If you want to obtain a stable (!) release, go to the [Releases](https://github.com/agnwinds/python/releases) page.
+If you want to obtain a stable (!) release, go to the [Releases](https://github.com/sirocco-rt/sirocco/releases) page.
 
 If you want to download the latest dev version, you can zip up the git repository by clicking on the zip icon to the right of the GitHub page. Aternatively, you can clone the repository using 
 
@@ -41,15 +42,15 @@ Note that the export syntax is for bash- for csh use
 Atomic data for the current version of Sirocco stored in the directory xdata which is part of the main repository,
 
 However, if one wishes to use model stellar spectra to simulate the spectra of the star or disk, one my wish to
-also to download various model grids of spectra that have been used in conjunction with Sirocco/Python over the years. These are in a separate [models repository]((https://github.com/agnwinds/xmod).  
+also to download various model grids of spectra that have been used in conjunction with Sirocco/Python over the years. These are in a separate [models repository]((https://github.com/sirocco-rt/xmod).  
 
 These can be downloaded as follows:
 
     $ cd $SIROCCO; git clone https://github.com/agnwinds/xmod xmod 
 
 (Previously, both the atomic data and the model grids were stored in a separate repository.  Users wishing
 to run older versions of the code pre-84b may need to download the 
-[old data repository](https://github.com/agnwinds/data)  This repository can be downloaded as follows
+[old data repository](https://github.com/sirocco-rt/data)  This repository can be downloaded as follows
 
 
     $ cd $SIROCCO; git clone https://github.com/agnwinds/data data
@@ -71,6 +72,6 @@ and run the code by typing, e.g.
     $ sirocco root.pf
 
 
-Please see the [ReadTheDocs](http://agnwinds.readthedocs.io/en/dev/) or the docs folder for how to use the code. You will need sphinx installed to build the documentation yourself. 
+Please see the [ReadTheDocs](http://sirocco-rt.readthedocs.io/en/dev/) or the docs folder for how to use the code. You will need sphinx installed to build the documentation yourself. 
 
 Any comments, email one of the addresses above.

configure

@@ -1,5 +1,5 @@
 #!/bin/sh
-# Shell script for configuring Python radiative transfer code compilation
+# Shell script for configuring Sirocco radiative transfer code compilation
 # James Matthews, University of Southampton
 # Questions: [email protected]
 # Usage: ./configure

docs/pydocs/README.md

@@ -2,3 +2,5 @@ This directory contains help files created from doc strings from
 python scripts in the py_progs directory.  
 
 To create the documentation yourself, simply run `write_docs.py`.
+
+This procedure should be largely superseded by https://agnwinds.readthedocs.io/en/dev/py_progs.html but that page is not currently complete.

docs/sphinx/requirements.txt

@@ -9,7 +9,7 @@ numpy
 matplotlib
 scipy
 sqlalchemy
-jinja2==3.0.3
+jinja2==3.1.4
 sphinx_gallery
 pyhdf
-sphinx-autoapi==3.1.1
+sphinx-autoapi==3.1.1

docs/sphinx/source/atomic.rst

@@ -1,19 +1,19 @@
 Atomic Data
 ###########
 
-Any Python model is only as good as the atomic data which goes into making the model.  
-All of the atomic data that Python accepts is read in by the routine get_atomicdata,
+Any SIROCCO model is only as good as the atomic data which goes into making the model.  
+All of the atomic data that SIROCCO accepts is read in by the routine get_atomicdata,
 and all of the data is read in from a series of ascii data files and stored in structures
 that are defined in atomic.h.
 
 
 The purpose of documentation is as follows:
 
-* to explain the atomic data formats used by Python and the relationship of different sets
+* to explain the atomic data formats used by SIROCCO and the relationship of different sets
   of data to one another
 
-* to explain where the data currently used in Python and to explain how the raw data 
-  is translated in to a format the Python accepts
+* to explain where the data currently used in SIROCCO and to explain how the raw data 
+  is translated in to a format the SIROCCO accepts
 
 The routines used to translate raw data format for two-level atoms (as well as much of the raw data)
 are contained in a separate github `repository <https://github.com/agnwinds/data-gen>`_
@@ -25,15 +25,15 @@ The routines used to generate data for MacroAtoms are described in :doc:`Generat
 
 Choosing a dataset 
 -----------------------
-The "masterfile" that determines what data will be read into Python is determined by the
+The "masterfile" that determines what data will be read into SIROCCO is determined by the
 line in the parameter file, which will read something like::
 
     Atomic_data                                data/standard80.dat
    
 where the file `data/standard80.dat` will contain names (one to a line) of files which will
 be read in sequentially.  
 
-All of the atomic data that comes as standard with Python is stored in the `xdata` directory (and its subdirectories) but users are not required to put their data
+All of the atomic data that comes as standard with SIROCCO is stored in the `xdata` directory (and its subdirectories) but users are not required to put their data
 there. Various experimental or testing dataset masterfiles are stored in the `zdata` directory. Symbolic links to these directories
 are setup by running `Setup_Py_Dir`.
 
@@ -44,7 +44,7 @@ are setup by running `Setup_Py_Dir`.
 Data hierarchy and I/O 
 -----------------------
 As mentioned above, the masterfile will contain names (one to a line) of files which will
-be read in sequentially. Every line in the atomic data files read by Python consists of a keyword that defines the type
+be read in sequentially. Every line in the atomic data files read by SIROCCO consists of a keyword that defines the type
 of data and various data values that are required for that particular data type.  Lines that
 beging with # or are empty are ignored.