Merge pull request #633 from agnwinds/dev

Pulling `dev` into `master` to create an official v84 release.

.gitignore

@@ -1,6 +1,10 @@
 # This is the git ignore for python
 # ignore binaries in bin/ such as e.g. py78a
 bin/py*
+bin/windsave2table*
+
+# Run files
+*.spec*
 
 # Object files
 *.o
@@ -33,17 +37,60 @@ bin/py*
 *.hex
 
 
-#things from gsl
+# things from gsl, may not be necessary
+software/gsl-2.5/Makefile
+software/gsl-2.5/*/Makefile
+software/gsl-2.5/*.dSYM
+software/gsl-2.5/*/*.dSYM
+software/gsl-2.5/bin/
+software/gsl-2.5/share/
+include/gsl/
+lib/pkgconfig/
+
+# the configure Makefile should not be tracked
+./Makefile
 
+# sphinx stuff
+docs/sphinx/html/
+docs/sphinx/doctrees/
 
+# doxygen stuff
+docs/doxygen/html/
+docs/doxygen/latex/
 
+# For if you're running py_progs in a virtual environment
+py_progs/venv/
+py_progs/*.html
+
+# For when the wiki is cloned locally
+wiki/
 
 # python and system files
 *.pyc
 *~
 *.DS_Store
 
-
 # some gsl files
 *.Plo
 *.Po
+
+# atomic data files should not be tracked by this repository
+data/
+
+# we shouldn't be tracking version.h either 
+source/version.h
+
+# python output files
+*.diag
+*.spec
+*.log_spec
+*.spec_tot
+*.log_spec_tot
+*.rdpar
+*.sig
+*.out.pf
+logfile
+
+# IDE files
+.idea/
+py_progs/.idea/

.readthedocs.yml

@@ -0,0 +1,23 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/sphinx/source/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/sphinx/requirements.txt

.travis.yml

@@ -22,17 +22,32 @@ compiler:
 branches:
   only:
     - dev
-    - enum
-    - domain2
+
+# specify email notifications
+notifications:
+  email:
+    recipients:
+      - [email protected]
+      - [email protected]
+      - [email protected]
+    on_success: never       # default: change
+    on_failure: always      # default: always
+
+# install numpy for test scripts
+before_install:                                                                                                                                                                                                                     
+  - sudo apt-get update -qq                                                                                                                                                                                                         
+  - sudo apt-get install -qq python3-numpy 
+  - sudo apt-get install -qq python3-astropy
 
 install:
     # first configure
     - export PYTHON=$TRAVIS_BUILD_DIR
-    - export PATH=$PATH:$PYTHON/bin 
+    - export PATH=$PATH:$PYTHON/bin:$PYTHON/py_progs
+    - export PYTHONPATH=$PYTHONPATH:$PYTHON/py_progs
     - ./configure
 
     # do installation
-    - make install
+    - make travis_install
 
 
     #Then clone data
@@ -44,17 +59,20 @@ script:
     - echo $PWD
     - cd source/
     - make clean
-    - make CC=gcc py_wind
+    - make CC=gcc INDENT=no py_wind
+    - make CC=gcc INDENT=no windsave2table
     - make clean
-    - cd ../examples/core/
+    - cd ../examples/travis/
     - Setup_Py_Dir
+    - py -f -v 1 balmer_test
+    - python3 ../../py_progs/balmer_decrement.py balmer_test
     - py -i cv_macro_benchmark
     - py -i cv_standard
-    - py -i -d sv_detailedmode
     - py -i fiducial_agn
     - py -i 1d_sn
-    - cd ../beta/
-    - py -i agn_ss_2010_modela.pf
+    - py -i -d sv_detailedmode
+    - py -i agn_ss_2010_modela
     - py -i ulx1
     - py -i ngc5548
     - py -i lamp_post
+    - py -i cv_standard_import

CITATION.cff

@@ -0,0 +1,60 @@
+cff-version: 1.0.3
+message: If you use Python, please cite both the software and the outline paper.
+authors:
+  - family-names: Long
+    given-names: Knox
+    orcid: https://orcid.org/0000-0002-4134-864X
+    affiliation: "Space Telescope Science Institute"
+    email: [email protected]
+  - family-names: Knigge
+    given-names: Christian
+    orcid: https://orcid.org/0000-0002-1116-2553
+    affiliation: "University of Southampton"
+    email: [email protected]
+  - family-names: Sim
+    given-names: Stuart
+    orcid: https://orcid.org/0000-0002-9774-1192
+    affiliation: "Queens University Belfast"
+    email: [email protected]
+  - family-names: Higginbottom
+    given-names: Nick
+    orcid: https://orcid.org/0000-0001-7560-4747
+    affiliation: "University of Southampton"
+    email: [email protected]
+  - family-names: Matthews
+    given-names: James
+    orcid: https://orcid.org/0000-0001-7560-4747
+    affiliation: "University of Oxford"
+    email: [email protected]
+  - family-names: Mangham
+    given-names: Sam
+    orcid: https://orcid.org/0000-0001-7511-5652
+    affiliation: "University of Southampton"
+    email: [email protected]
+  - family-names: Parkinson
+    given-names: Edward
+    orcid: https://orcid.org/0000-0003-3902-052X
+    affiliation: "University of Southampton"
+    email: [email protected]
+  - family-names: Hewitt
+    given-names: Mandy
+    affiliation: "Queens University Belfast"
+    email: [email protected]
+website: https://github.com/agnwinds/python
+title: Python
+version: 83b
+# doi: ??.?/zenodo.????
+date-released: 2019-02-24
+references:
+  - type: article
+    authors:
+      - family-names: Long
+        given-names: Knox
+      - family-names: Knigge
+        given-names: Christian
+    title: "Modeling the Spectral Signatures of Accretion Disk Winds: A New Monte Carlo Approach"
+    year: 2002
+    journal: The Astrophysical Journal
+    volume: 579
+    issue: 2
+    doi: 10.1086/342879