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Oldphysics docs #3

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ff6c04c
Initial commit
epassaro Oct 27, 2020
d5b60b0
add token
epassaro Oct 27, 2020
3be30a4
add push step
epassaro Oct 27, 2020
efe3ba5
add cron trigger for doc pipeline
epassaro Oct 27, 2020
eef40f5
change job name
epassaro Oct 27, 2020
7a2a501
add comment block
epassaro Oct 27, 2020
9102446
commit with bot account
epassaro Nov 9, 2020
e0053be
Fix to virtual packet logging
andrewfullard Nov 18, 2020
69fd1ed
Inside of tardis/docs/pphysics/plasma/plasma_plots updated two files …
KevinCawley Nov 20, 2020
307a2d2
Some more documentation updates
KevinCawley Nov 22, 2020
460e793
Finished issue #680
KevinCawley Nov 22, 2020
76b7ae5
Merge pull request #2 from KevinCawley/documentation
KevinCawley Nov 22, 2020
df2e719
Fixed the last file for #680
KevinCawley Nov 22, 2020
ef40bb3
Merge pull request #3 from KevinCawley/documentation
KevinCawley Nov 22, 2020
a2a36e6
Fixed two random indentation irregularities found upon review
KevinCawley Nov 25, 2020
9d66023
Update to fork
KevinCawley Nov 25, 2020
56c5067
Merge pull request #4 from KevinCawley/documentation
KevinCawley Nov 25, 2020
a1e5633
Another test
KevinCawley Nov 25, 2020
ff2199b
restructuring docs except for using tardis section
isaacgsmith Nov 27, 2020
32e7841
fixing old_physics
isaacgsmith Nov 27, 2020
bafa776
adding alumni section and other team and governance corrections
isaacgsmith Nov 27, 2020
9c98722
adding team_and_governance index file
isaacgsmith Nov 29, 2020
3283db4
Fixing issue #1177 (#1361)
isaacgsmith Nov 30, 2020
6564a5e
Fix of Issue #680 (#1359)
KevinCawley Nov 30, 2020
686617e
Merge remote-tracking branch 'upstream/master' into issue_1357_fix
isaacgsmith Nov 30, 2020
765745e
restructuring components and GUI subsections
isaacgsmith Dec 1, 2020
bbddc40
restructuring additional interactivity section and changing the order…
isaacgsmith Dec 1, 2020
303c7e1
Fixed to the montecarlo_numba file to compy w/ issue #680
KevinCawley Dec 2, 2020
d51b7f9
Initial numba parallelization
andrewfullard Dec 2, 2020
c3b5fa1
Fixed the latex equation
KevinCawley Dec 2, 2020
ebe33c5
adding andrew to tardis core
isaacgsmith Dec 3, 2020
1fa9dce
Made scalars overwrite & added option to control overwriting
jaladh-singhal Dec 4, 2020
a7f6050
Added overwrite option in docstrings and fixed them
jaladh-singhal Dec 4, 2020
aa37e1e
Added overwrite=True option in tests using hdfs
jaladh-singhal Dec 4, 2020
080552b
Fixed a typo in docstring
jaladh-singhal Dec 4, 2020
5ae8d7c
Merge pull request #1364 from smithis7/issue_1357_fix
andrewfullard Dec 4, 2020
722392f
Improved docstrings
jaladh-singhal Dec 4, 2020
077cfe7
Removed buf_opened flag since buf.is_open has that info
jaladh-singhal Dec 4, 2020
1249c4e
Merge pull request #1366 from jaladh-singhal/hdf-scalars-fix
andrewfullard Dec 4, 2020
176a632
First start on the two .rst files for the issues
KevinCawley Dec 5, 2020
5b4265b
Update to progress on this branch
KevinCawley Dec 6, 2020
5a6b518
Added note about ion 0 is neutral
KevinCawley Dec 6, 2020
f6f53f7
Trying to fix merge conflict
KevinCawley Dec 6, 2020
13ede90
Merge branch 'master' into Issue_1176_good
KevinCawley Dec 6, 2020
f56017d
Update base.py
KevinCawley Dec 6, 2020
2275f72
Update atomic.py
KevinCawley Dec 6, 2020
073c581
Update datahandler.py
KevinCawley Dec 6, 2020
6a26d57
revert to conf.py
KevinCawley Dec 6, 2020
a82ccd3
Merge branch 'master' into Issue_1154
KevinCawley Dec 6, 2020
2ee46b2
Remove extra carriage return
KevinCawley Dec 6, 2020
af2f6b3
slight update to the file
KevinCawley Dec 6, 2020
4c534c2
deleting unused files
isaacgsmith Dec 1, 2020
82f171e
reorganizing docs/running
isaacgsmith Dec 3, 2020
b9a5ef6
clarifying which file to use in toctree, as there is a to_hdf.rst and…
isaacgsmith Dec 3, 2020
74d1c1f
fixing new_plasma toc
isaacgsmith Dec 4, 2020
5f3edbc
fixing headers on outdated sections
isaacgsmith Dec 4, 2020
3ff6efa
adding custom_source and physical_quantities to additional interactiv…
isaacgsmith Dec 4, 2020
84d0e1c
removing physical_quantities from old_physics
isaacgsmith Dec 4, 2020
3d29959
fixing heading on CONTRIBUTING.md
isaacgsmith Dec 6, 2020
ac98ba8
adding using_formal_integral
isaacgsmith Dec 6, 2020
4a6793c
Merge pull request #1331 from epassaro/action-changelog
andrewfullard Dec 7, 2020
186351c
Merge pull request #1365 from andrewfullard/numba-parallel-patch
andrewfullard Dec 8, 2020
29685d8
Merge pull request #1368 from KevinCawley/Issue_1176_good
andrewfullard Dec 8, 2020
fc1798b
update to the docs
KevinCawley Dec 8, 2020
227af89
Merge remote-tracking branch 'upstream/master'
KevinCawley Dec 8, 2020
16362df
fix merge conflict
KevinCawley Dec 8, 2020
28e161a
doing Jaladh's suggestions
isaacgsmith Dec 8, 2020
25c9390
vpacket logging now suitable for kromer plot
andrewfullard Dec 9, 2020
61d7289
black applied
andrewfullard Dec 9, 2020
1008b9b
Fix test to match new style
andrewfullard Dec 9, 2020
7fa5d16
Merge pull request #1354 from tardis-sn/virt-packet-logging-fix
andrewfullard Dec 9, 2020
a49e4cc
Fixed rpacket logging of properties
andrewfullard Dec 9, 2020
bb0a1b4
Merge pull request #1375 from andrewfullard/rpacket-logging-fix
andrewfullard Dec 9, 2020
da51efa
Update CI doc section (#1372)
epassaro Dec 9, 2020
1c706d5
Merge pull request #1371 from smithis7/cleaning_docs
andrewfullard Dec 9, 2020
5236056
fixing mistake
isaacgsmith Dec 9, 2020
1597b1c
renaming running to using
isaacgsmith Dec 6, 2020
6565a80
Merge pull request #1378 from smithis7/fixing_index
andrewfullard Dec 9, 2020
8c53894
fixing merge conflict
isaacgsmith Dec 6, 2020
3ac370b
changing tardis_widgits to gui
isaacgsmith Dec 6, 2020
002e635
turning tardis_widgits into gui on docs/index.rst
isaacgsmith Dec 6, 2020
683d5d7
putting models in using/components
isaacgsmith Dec 7, 2020
e358411
adding configuration to docs/using/components
isaacgsmith Dec 8, 2020
140d540
adding atomic to docs/using/components
isaacgsmith Dec 8, 2020
9ffee87
fixing hyperlink in quickstart
isaacgsmith Dec 8, 2020
2def773
FIx real packet logging for last interaction type
andrewfullard Dec 11, 2020
613527a
Virtual packet logging fix
andrewfullard Dec 11, 2020
ce5b665
Merge pull request #1379 from smithis7/reorganizing_2
andrewfullard Dec 11, 2020
3c2b83b
fixing quickstart problem
isaacgsmith Dec 11, 2020
162f280
Merge pull request #1382 from smithis7/build_problem
andrewfullard Dec 11, 2020
d4c74f1
Possible fix for vpacket last interaction spectrum
andrewfullard Dec 14, 2020
77c2782
Small fixes for existing workflows (#1384)
epassaro Dec 14, 2020
1710023
Update tardis/montecarlo/montecarlo_numba/single_packet_loop.py
andrewfullard Dec 15, 2020
4a509b6
Update tardis/montecarlo/montecarlo_numba/single_packet_loop.py
andrewfullard Dec 15, 2020
575c228
Merge pull request #1380 from andrewfullard/packet-logging-oatch
andrewfullard Dec 15, 2020
6ec4b8f
Added modified kromer plot to work with widgets
jaladh-singhal Jul 17, 2020
5b6a635
Converted SimulationKromerPlotter to class method
jaladh-singhal Jul 23, 2020
f7503ee
Added missing required properties to save in hdf
jaladh-singhal Jul 28, 2020
02f9500
Added classmethod to create plotter from hdf
jaladh-singhal Jul 28, 2020
8957afe
Added docstrings to data attributes
jaladh-singhal Jul 29, 2020
dd7c2d6
Simplified Kromer Plotter with new structure
jaladh-singhal Oct 20, 2020
48ac765
Added relevant properties which need to be saved
jaladh-singhal Oct 29, 2020
ce88c67
Added KromerPlotter to init
jaladh-singhal Oct 29, 2020
415e360
Added classmethod for reading data from hdf
jaladh-singhal Oct 30, 2020
1ee0535
Renamed spectrum_frequency to spectrum_frequency_bins
jaladh-singhal Oct 30, 2020
25ae720
Added docstrings to data handling methods
jaladh-singhal Oct 30, 2020
d53b080
Isolated plotting and calculation code in generate_plot
jaladh-singhal Nov 5, 2020
a26d49a
Removed redundant calculation of packet_nu_range_mask
jaladh-singhal Nov 6, 2020
dc948e8
Separated calculation code in a different method
jaladh-singhal Nov 6, 2020
4ee827e
Added plolty plotting methods
jaladh-singhal Nov 7, 2020
59e9a65
Made dedicated method for showing colorbar in plotly & mpl
jaladh-singhal Nov 7, 2020
41a3cb5
Used plot_util to make labels render in plotly
jaladh-singhal Nov 10, 2020
1714e13
Reduce fontsize of mpl plot labels
jaladh-singhal Nov 10, 2020
2584ed4
Fixed problems in plot when packet_wvl_range is used
jaladh-singhal Nov 12, 2020
02fff16
Reordered methods to group related methods sequentially
jaladh-singhal Nov 12, 2020
ecd709a
Added docstring to calculation method & improved masking
jaladh-singhal Nov 12, 2020
a58869f
Added docstrings to KromerPlotter methods
jaladh-singhal Nov 13, 2020
af4380a
Made test_spectrum to handle hdf saving of scalars
jaladh-singhal Dec 15, 2020
943bab3
Fixing docs building problem (#1387)
isaacgsmith Dec 16, 2020
0c09399
Revert "Fixing docs building problem (#1387)" (#1394)
andrewfullard Dec 16, 2020
23ac153
Fix documentation build (#1392)
epassaro Dec 16, 2020
be92206
adding title to current_public_table.rst
isaacgsmith Dec 17, 2020
9493122
removed the nbsphinx_allow_errors = True
KevinCawley Dec 17, 2020
b315927
Update to fix merge conflitcs
KevinCawley Dec 17, 2020
f401f05
fixing merge conflicts
KevinCawley Dec 17, 2020
c950345
add preview docs section (#1383)
epassaro Dec 17, 2020
93eaa7c
fixing some hyperlinks
isaacgsmith Dec 17, 2020
19717f8
adding label to physical_quantities
isaacgsmith Dec 18, 2020
3f722e8
fixing links in to_hdf
isaacgsmith Dec 18, 2020
04a5f9c
fixing more links
isaacgsmith Dec 18, 2020
49652c9
fixing header on montecarlo_old
isaacgsmith Dec 18, 2020
b6c35fb
trying to fix my branch
KevinCawley Dec 18, 2020
a8450ea
Merge branch 'Issue_1252_1170' of github.com:KevinCawley/tardis into …
KevinCawley Dec 18, 2020
43129af
trying to fix merge conflicts
KevinCawley Dec 18, 2020
7bc3afb
Removed commented debugging code & added newlines at EOF
jaladh-singhal Dec 18, 2020
a4d6003
updates to these two files
KevinCawley Dec 18, 2020
cadccff
Fix incorrect docstrings (#1369)
KevinCawley Dec 18, 2020
2d9ada5
Update Matterbridge docs (#1395)
epassaro Dec 18, 2020
ccbd676
will this fix work
KevinCawley Dec 19, 2020
77dabb2
Fixing merge conflicts
KevinCawley Dec 19, 2020
0fa6de4
work done on docs
KevinCawley Dec 19, 2020
3570427
Merge branch 'Issue_1252_1170' of github.com:KevinCawley/tardis into …
KevinCawley Dec 19, 2020
398f588
Updates to files, testing out display in tardis
KevinCawley Dec 19, 2020
91616bb
removed random sn
KevinCawley Dec 20, 2020
373b0d5
trying to get documentation to build
KevinCawley Dec 20, 2020
dc87c67
fixing some indentation and syntax errors
KevinCawley Dec 20, 2020
db06eb6
fix of syntax for local compile, and removed section of index where t…
KevinCawley Dec 20, 2020
16f24cd
Fixed missing file
KevinCawley Dec 20, 2020
588fda7
changes to make proper syntax
KevinCawley Dec 20, 2020
f96c2fd
trying to fix syntax
KevinCawley Dec 20, 2020
bf8f7ad
Merge pull request #1241 from jaladh-singhal/widgets/kromer_plot
marxwillia Dec 21, 2020
9885897
Update to docs on code quality and guidelines
KevinCawley Dec 22, 2020
e11ae86
Merge remote-tracking branch 'upstream/master' into Issue_1252_1170
KevinCawley Dec 22, 2020
bfad2c8
Update to files descriptions and explanations, fixed grammar
KevinCawley Dec 26, 2020
7fbf0c7
add parso
epassaro Dec 27, 2020
e8ef961
Explicitly add parso to dependencies
andrewfullard Dec 28, 2020
7ee2a08
fix tests with --generate-reference flag
epassaro Dec 22, 2020
84460c4
add black check workflow
epassaro Dec 21, 2020
dabe080
reformatted files
epassaro Dec 29, 2020
3c6395f
added functionality for automatic date updation in docs & fixed the 2…
DhruvSondhi Dec 30, 2020
58e3255
Added section of edge cases and exception handling
KevinCawley Dec 30, 2020
07605cb
Delete Documentation_Guidelines.rst
KevinCawley Dec 30, 2020
68f975a
Delete building_local_docs.rst
KevinCawley Dec 30, 2020
07c663c
Delete coding_guide.rst
KevinCawley Dec 30, 2020
e8df255
Added naming conventions to its own section as it's important
KevinCawley Dec 30, 2020
0713ed3
Merge branch 'Issue_1252_1170' of github.com:KevinCawley/tardis into …
KevinCawley Dec 30, 2020
4bd4f80
Copyright date automatically updates pr/1404
andrewfullard Jan 5, 2021
369a664
Update git_workflow.rst
KevinCawley Jan 6, 2021
fc6af1d
Update index.rst
KevinCawley Jan 6, 2021
cf78251
Update numba_interface.py
KevinCawley Jan 6, 2021
2c6e472
Update r_packet.py
KevinCawley Jan 6, 2021
9b5e21a
Update single_packet_loop.py
KevinCawley Jan 6, 2021
e2243ce
update env file (#1393)
epassaro Jan 8, 2021
9c5e24c
Fix tests with --generate-reference flag
andrewfullard Jan 8, 2021
9ab7de7
initial commit
epassaro Jan 12, 2021
c741faa
Update docs/Code_Quality_Guidelines.rst
KevinCawley Jan 18, 2021
cf1b367
Update docs/Code_Quality_Guidelines.rst
KevinCawley Jan 18, 2021
30762d1
Update numba_interface.py
KevinCawley Jan 18, 2021
6e63544
Update numba_interface.py
KevinCawley Jan 18, 2021
0656db1
Update r_packet.py
KevinCawley Jan 18, 2021
0fbdf1d
Update single_packet_loop.py
KevinCawley Jan 18, 2021
586ea43
Update packet_source.py
KevinCawley Jan 18, 2021
ca81bd5
Restructured developer workflow toctrees
jaladh-singhal Jan 20, 2021
a2324e5
Moved documentation guidelines to a separate rst file
jaladh-singhal Jan 20, 2021
f2e82f8
Add black check workflow
andrewfullard Jan 20, 2021
86d8945
Corrected the Hyperlink reference
himanshu007-creator Jan 21, 2021
8f9a0fd
Edited documentation guidelines
jaladh-singhal Jan 21, 2021
5078bf4
Added running tests to index
jaladh-singhal Jan 21, 2021
8522e7c
blackify tests
epassaro Jan 21, 2021
98a6840
Corrected quickstart hyperlink
andrewfullard Jan 21, 2021
7d7c4bc
Black formatting applied to tests
andrewfullard Jan 21, 2021
fe10159
Add .log to gitignore, disabled montecarlo log
andrewfullard Jan 21, 2021
ae19c5f
Edited code quality guidelines
jaladh-singhal Jan 21, 2021
25c3193
Inserted missing links in Contributing.md
jaladh-singhal Jan 21, 2021
b941dc2
two more fixed hyperlinks
isaacgsmith Jan 22, 2021
54cc315
adding old_plasma section to toctree
isaacgsmith Jan 25, 2021
66f3d8f
moving old_plasma to under old_physics
isaacgsmith Jan 25, 2021
1e87cf6
moving old_plasma file
isaacgsmith Jan 25, 2021
12d9ebb
Add .log to gitignore, disabled montecarlo log
andrewfullard Jan 25, 2021
9cab1ba
Post reference data results
andrewfullard Jan 25, 2021
077ec99
Update PULL_REQUEST_TEMPLATE.md
marxwillia Jan 25, 2021
6a8403b
Fixing Hyperlinks in Documentation
andrewfullard Jan 25, 2021
98baa39
Fix for int64 datatype of variables
DhruvSondhi Jan 24, 2021
4a6a8a6
Fix for packet output data types
andrewfullard Jan 25, 2021
5ecd64f
removing plasma/index
isaacgsmith Jan 25, 2021
cb25fa6
switching physics/plasma.rst to physics/plasma/index.rst
isaacgsmith Jan 25, 2021
9dd0098
fixing hyperlink problems that arose from changes
isaacgsmith Jan 25, 2021
d6e2457
changing hyperlink text
isaacgsmith Jan 25, 2021
234ae1b
fixes for ci docs
epassaro Jan 26, 2021
4f57e74
CI documentation fixes
andrewfullard Jan 26, 2021
0c8602d
Old physics docs reorganization
andrewfullard Jan 26, 2021
abc53ff
Update code_quality.rst
KevinCawley Jan 26, 2021
1d6100b
Update documentation_guidelines.rst
KevinCawley Jan 26, 2021
600de0e
Update documentation_guidelines.rst
KevinCawley Jan 26, 2021
3216283
Update code_quality.rst
KevinCawley Jan 26, 2021
a6d190c
Restructured development workflow and added code quality & documentat…
andrewfullard Jan 27, 2021
72fd51c
add docstr-coverage workflow (#1409)
epassaro Jan 27, 2021
68bc12a
Rename Kromer Plot to Spectral Element Decomposition (SEDec) Plot (#1…
jaladh-singhal Jan 28, 2021
6f89804
Documentation guidelines hotfix (#1431)
KevinCawley Jan 28, 2021
1053c90
compare refdata with arbitrary labels (#1430)
epassaro Jan 28, 2021
4c346f0
Rename SEDec to SDEC in Spectral element DEComposition plot (#1441)
jaladh-singhal Jan 29, 2021
3ac1435
fix update changelog workflow (#1432)
epassaro Jan 30, 2021
7f31e2b
Fixed distance parameter not producing accurate SDEC plots (#1442)
jaladh-singhal Feb 1, 2021
6a271f1
numba_warning (#1455)
antreev-brar Feb 10, 2021
b9ab7c8
Add documentation for Spectral Element Decomposition Plot (#1438)
jaladh-singhal Feb 11, 2021
b2b6a6f
Fixed italicised Units in sdec_plot (#1446)
DhruvSondhi Feb 12, 2021
0a18018
Re-generated SDEC plots
jaladh-singhal Feb 12, 2021
7f98210
Merge pull request #1457 from jaladh-singhal/sdec-replot
marxwillia Feb 12, 2021
8d2c62a
Added option to create redirects in docs configuration and redirected…
jaladh-singhal Feb 16, 2021
927c606
Reorganizing Models (#1454)
isaacgsmith Feb 17, 2021
d92464c
Fix the array types when interpolate_shells > 0
Rodot- Feb 19, 2021
50f13ba
Renamed widgets subpackage to visualization and restructured modules …
jaladh-singhal Feb 24, 2021
bc1707c
incorporating old_physics
isaacgsmith Feb 26, 2021
e080bb8
Update documentation-build.yml
isaacgsmith Feb 28, 2021
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trying to fix my branch
  • Loading branch information
KevinCawley committed Dec 18, 2020
commit b6c35fb41044fa42fe2160e7f82c56426954ca89
2 changes: 1 addition & 1 deletion .github/workflows/documentation-build.yml
Original file line number Diff line number Diff line change
@@ -21,7 +21,7 @@ jobs:
with:
environment-file: tardis_env3.yml
activate-environment: tardis
channels: conda-forge, defaults
channels: conda-forge
mamba-version: "*"

- name: Install TARDIS
1 change: 1 addition & 0 deletions .github/workflows/update-changelog.yml
Original file line number Diff line number Diff line change
@@ -23,6 +23,7 @@ jobs:
- name: Commit files
run: |
git config --local user.email "[email protected]"
git config --local user.name "TARDIS bot"
git add CHANGELOG.md
git commit -m "Update CHANGELOG.md [skip ci]"

2 changes: 1 addition & 1 deletion CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Contributing to TARDIS
# Contribution Guidelines

So you are wondering how can you contribute to TARDIS? Congrats, you've landed on the right page!

21 changes: 21 additions & 0 deletions docs/building_local_docs.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
##################
Building Local Docs
##################


Building local docs is done via compiling docs locally. In order to do this, go into the tardis/docs/conf.py file. Create a new line before line 81. Line 80 is::

# -- General configuration ----------------------------------------------------

In the new line, type "nbsphinx_allow_errors = True". After this, the code should now look like this::

nbsphinx_allow_errors = True
# -- General configuration ----------------------------------------------------

Do not push a commit or make a PR that has the change to tardis/docs/conf.py added.

Once this is done, in the terminal inside the main tardis folder, type "python setup.py build_docs". This should create a new folder, _build, inside tardis/docs. Go through this folder and find the local docs that you are changing/creating to view how they will be compiled once a PR is approved. This method is good to check the formatting of docstrings in the API and the formatting of display files such as this one, as well as any other aspects that will be loaded in the tardis docs.

For information on how docstrings should be formatted, refer 'here <https://tardis-sn.github.io/tarids/coding_guidelines.html>`_ for more information and examples. To create new documentation that will have a link inside the `TARDIS pages <https://tardis-sn.github.io/tardis>`_, you will need to edit the corresponding index.rst file to include your file inside of the toctree. For example, when the documentation was made for `research papers <https://tardis-sn.github.io/tardis/research/research_done_using_TARDIS/research_papers.html>`_ that used TARDIS, this location's `index.rst <https://github.com/tardis-sn/tardis/blob/master/docs/research/index.rst>`_ toctree was editted to include the path to the .rst file that would be generated when the docs are compiled and create a notebook.

When making or adding to the functionality of an aspect of TARDIS, an example notebook file should be made to show the changes/function that is created using that file. If a file is being converted from one language to another, a notebook should be included to show that the same values are outputted.
35 changes: 35 additions & 0 deletions docs/coding_guide.rst
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
##################
TARDIS Coding Guide
##################


TARDIS follows the `Black <https://black.readthedocs.io/en/stable/>`_ coding style for files. To install Black, do::

pip install black

For more information on Black, please refer to `Black <https://black.readthedocs.io/en/stable/>`_.

For docstrings, TARDIS follows the docstring formatting of `Numpydocs <https://numpydoc.readthedocs.io/en/latest/format.html>`_.
This is an example of a properly formatted docstring::
"""
read different density file formats

Parameters
----------
filename : str
filename or path of the density file
filetype : str
type of the density file

Returns
-------
time_of_model : astropy.units.Quantity
time at which the model is valid
velocity : np.ndarray
the array containing the velocities
unscaled_mean_densities : np.ndarray
the array containing the densities
"""
The docstring should have no leading or trailing carriage returns, and there should be a carriage return between each segment. If the function does not have a return statement, then the Returns section is not necessary.

For the naming conventions in TARDIS, please follow the naming conventions of `PEP8 <https://www.python.org/dev/peps/pep-0008/#naming-conventions>`_. Taken from PEP8, "Function names should be lowercase, with words separated by underscores as necessary to improve readability. Variable names follow the same convention as function names. Class names should normally use the CapWords convention." For more detailed information on naming conventions, please refer to the `PEP8 <https://www.python.org/dev/peps/pep-0008/#naming-conventions>`_ guide.
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125 changes: 62 additions & 63 deletions docs/development/continuous_integration.rst
Original file line number Diff line number Diff line change
@@ -9,22 +9,13 @@ clone the repository, checkout to the current commit and execute
all the TARDIS tests. This helps us to detect bugs immediately.


Azure Pipelines
===============

Currently, we use the `Azure DevOps`_ service to run most of our
pipelines. The following section explains briefly the different
components of a pipeline.


Repos
-----
Azure Repos
-----------

Azure Repos is just another service to store Git repositories.
Currently, we use Azure Repos to mirror ``tardis-refdata``
repository since Azure does not impose limits on LFS bandwith
nor storage. We should sync this mirror every time reference
data is updated on GitHub.
nor storage.

**To clone this repository:**
::
@@ -34,24 +25,36 @@ data is updated on GitHub.
::
https://dev.azure.com/tardis-sn/TARDIS/_apis/git/repositories/tardis-refdata/items?path=atom_data/kurucz_cd23_chianti_H_He.h5&resolveLfs=true

This mirror is automatically synced by `a GitHub workflow`_. If you want
to `update it manually`_, remember to set ``git config http.version HTTP/1.1``
to avoid `error 413`_ while pushing large files.


Azure Pipelines & GitHub Actions
--------------------------------

YAML files
----------
Currently, we use the `Azure DevOps`_ service to run most of our
pipelines and GitHub Actions for some others (called "workflows"). The
following sections explains briefly the different components of a
pipeline/workflow, mostly focused on the Azure service.

A pipeline (or a workflow) is essentially a YAML configuration file
with different sections such as variables, jobs and steps. These files
run commands or tasks when they are triggered by some event, like a
commit being pushed to a certain branch.

A pipeline is essentially a YAML configuration file with different
sections such as variables, jobs and steps. Unlike other services
such as GitHub Actions, pipelines on Azure must be created through
the web UI for the first time. Then, making changes to an existing
pipeline is as easy as making a pull request.
Pipelines on Azure must be created through the web UI for the first time.
Then, making changes to an existing pipeline is as easy as making a pull
request. To create a new workflow on GitHub, just create a new YAML file
in ``.github/workflows``.


Triggers
--------

First thing to do is telling the pipeline when it should run.
*trigger* (also known as the CI trigger) sets up the pipeline to
run every time changes are merged to the *master* branch.
First thing to do is telling the pipeline when it should run. In
Azure, *trigger* (also known as the CI trigger) sets up the pipeline
to run every time changes are pushed to a branch.
::
trigger:
- master
@@ -69,11 +72,11 @@ is assumed.
include:
- '*'

This means the pipeline will start running every time changes are
This means the pipeline will start running every time changes are
merged to any branch of the repository, or someone pushes new
commits to a pull request.

If you want to run a pipeline only manually set both triggers to
If you want to run a pipeline only manually set both triggers to
*none*.
::
trigger: none
@@ -84,20 +87,23 @@ Notice that you can test changes in a pipeline by activating the PR
trigger on a new pull request, even if that trigger is disabled on
the YAML file present in the *master* branch.

There are more useful triggers such as the *cron* trigger, see the
`Azure documentation section on triggers`_ for more information.
On GitHub Actions these triggers are named ``push`` and ``pull_request``,
and works mostly in the same way.

.. warning:: Triggers also can be set on the Azure's web interface
.. warning:: Triggers also can be set on the Azure's web interface
too, but this action is discouraged, since it overrides
any trigger specified in the YAML file and could lead to
confusing sitations.

There are more useful triggers such as the *cron* trigger, see the
`Azure documentation section on triggers`_ for more information.


Variables
---------

Variable syntax
***************
===============

Azure Pipelines supports three different ways to reference variables:
*macro*, *template expression*, and *runtime expression*. Each syntax
@@ -113,7 +119,7 @@ use a *template expression*.


Define variables
****************
================

Usually, we define variables at the top of the YAML file.
::
@@ -172,9 +178,6 @@ to paths in Azure:
See the Azure documentation to learn more about `checking out multiple repositories`_.


Azure provides a list of agent hosts that can run the pipeline on a virtual machine. In our pipelines, we
use the vm_Images: Ubuntu 16.04 and macOs-10.14.

Jobs
----

@@ -200,32 +203,26 @@ See the `Azure documentation section on jobs`_ for more information.
.. include:: azure_links.inc


Templates
---------

Templates let you define reusable content, logic, and parameters. It functions
like an include directive in many programming languages (content from one file
is inserted into another file).

See the `Azure documentation section on templates`_ for more information.


TARDIS Pipelines
================
----------------

Already implemented on Azure or GitHub Actions.
Brief description of pipelines already implemented on Azure or GitHub Actions.


Default template
----------------
The default template
====================

Templates let you define reusable content, logic, and parameters. It functions
like an include directive in many programming languages (content from one file
is inserted into another file).

The common set of steps used across most TARDIS pipelines now lives in the
"default" template.
The common set of steps used across most TARDIS pipelines resides in the
"default" template:

- Use ``set -e`` on Bash steps.
- Set custom variables.
- Force ``set -e`` on all Bash steps.
- Set TARDIS custom variables.
- Fetch TARDIS main repository.
- Fetch TARDIS reference data repository (optional).
- Fetch TARDIS reference data repository from mirror (optional).
- Configure Anaconda for Linux and macOS agents.
- Install Mamba package manager (optional).
- Install TARDIS environment (optional).
@@ -253,24 +250,26 @@ to start a new pipeline use::
- ``tardis.dir`` is equivalent to ``$(Build.SourcesDirectory)/tardis``.
- ``refdata.dir`` is equivalent to ``$(Build.SourcesDirectory)/tardis-refdata``.

See the `Azure documentation section on templates`_ for more information.


Documentation pipeline
======================

Builds and deploys the TARDIS documentation website. Currently, we use
GitHub Actions for this purpose.


Testing pipeline
----------------
================

The `testing pipeline`_ (CI) consists basically in the same job running twice
in parallel (one for each OS) with the steps from the default template, plus
extra steps to run the tests and upload the coverage results.


Documentation pipeline
----------------------

Builds and deploys the TARDIS documentation website. Currently, we are
using GitHub Actions for this purpose.


Zenodo JSON pipeline
--------------------
Authors pipeline
================

This pipeline runs a notebook located in ``tardis-zenodo`` repository and
pushes a new version of ``.zenodo.json`` to the root of ``tardis``
@@ -286,13 +285,13 @@ In the near future we want to auto-update the citation guidelines in the


Release pipeline
----------------
================

Publishes a new release of TARDIS every sunday at 00:00 UTC.


Reference data pipeline
-----------------------
=======================

Generates new reference data according to the changes present in the
current pull request. Then, compares against reference data present in the
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