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718c4b8
Update comments
penmaher Jan 29, 2021
454659a
Updates for gibbs fix
penmaher Jan 29, 2021
c4dbeb4
New exp for clouds and topo
penmaher Jan 29, 2021
61c095c
Testing the Gibbs fix
penmaher Feb 2, 2021
5ae287e
Documentation page on the structure of Isca and comparison to the 200…
rosscastle Feb 3, 2021
9618e94
units correction for ucomp_height
lqxyz Feb 4, 2021
433ec43
Merge pull request #202 from lqxyz/units_correct
lqxyz Feb 4, 2021
daded8f
Updated to include file in index menu.
Feb 11, 2021
b134db8
Merge pull request #169 from mckimb/brettm
mckimb Feb 11, 2021
f4b57f6
Testing cloud scheme in Isca
penmaher Feb 22, 2021
d4ca702
Added more information about how to compute q-fluxes
penmaher Feb 24, 2021
e4e8e7e
Changes made from PM, NL, MH. Typos fixed and clarifications made in …
rosscastle Mar 1, 2021
f509f7c
Changed the shell script from moab to slurm as the ISCA HPC has been …
rosscastle Mar 2, 2021
a31eaa5
Update isca_job.sh
rosscastle Mar 9, 2021
8c1c696
Update isca_job.sh
rosscastle Mar 11, 2021
2b603fa
Merge pull request #204 from rosscastle/hpc_script
rosscastle Mar 11, 2021
66fae9c
Updated to address comments in PR and tidy formatting.
Mar 15, 2021
a9b5810
Add files via upload
rosscastle Mar 31, 2021
6184fb9
Update index.rst
rosscastle Mar 31, 2021
130dcba
Update begginers_guide.rst
rosscastle Apr 1, 2021
dcd2e7a
Update begginers_guide.rst
rosscastle Apr 1, 2021
8133f09
Reduce smoothing for amip topo with original era land. Need to check …
penmaher Apr 12, 2021
36292a0
Testing topohraphy
penmaher Apr 26, 2021
fb8ac3c
Update install.rst
rosscastle Apr 28, 2021
ed692a0
Draft surface_flux module docs
May 19, 2021
3c8ad54
Update branch in line with master
May 19, 2021
9dc81eb
Merge pull request #201 from rosscastle/docs_structure
rosscastle May 19, 2021
3686615
Complete first draft of surface_flux_mod docs
May 19, 2021
a9c8f5d
Typo fixed
rosscastle May 19, 2021
00b6df8
Merge in the Head of the Isca master into my local cloud dev branch
penmaher May 21, 2021
a6610c3
Revert experiement changes so code can be merged onto the master
penmaher May 21, 2021
4c1ffb3
Testing with MiMA was not sufficiently done, so I am removing the tes…
penmaher May 21, 2021
005ea3d
Revert files which were for local testing only and should not be on m…
penmaher May 21, 2021
3ee76fd
Revert run script to master version but kept the changes to the file …
penmaher May 21, 2021
ba8c8bb
Ruth suggested I add the output nc file into this PR. The script used…
penmaher May 21, 2021
f56e8d7
Update begginers_guide.rst
rosscastle May 21, 2021
dcf2af3
Update begginers_guide.rst
rosscastle May 21, 2021
f4f0bf3
Update conf.py
rosscastle May 21, 2021
15f9b25
Changes to code folling the review by Qun. Should not change the scie…
penmaher Jun 11, 2021
6ac66f1
Following review, these changes were needed to make the model compile…
penmaher Jun 11, 2021
927e3d5
Make file names more meaningful and made experiment names more general
penmaher Jun 11, 2021
f95b018
Minor style changes to code following Quns second review
penmaher Jun 22, 2021
b0d088a
Changed path in travis tests following Denis suggestion
penmaher Jun 24, 2021
9b74061
Add socrates cloud test case to trip tests
penmaher Jun 24, 2021
12cd890
Add fatal error to catch the case the RRTM might be run with clouds o…
penmaher Jun 24, 2021
cceda96
Add clouds to grey path names but it does not yet work for grey scheme
penmaher Jun 24, 2021
84cf8c4
Added a fatal error if someone tried to run the clouds scheme and gre…
penmaher Jun 24, 2021
7d2f0ab
Added context to explain that cloud scheme does not work for RRTM but…
penmaher Jun 24, 2021
c93bc97
Added cloud scheme in dry path name list as it calls idealised moist …
penmaher Jun 25, 2021
5dc49a6
Added cloud scheme in dry path name list as it calls idealised moist …
penmaher Jun 25, 2021
a058559
Script to look for the fortran files that contain namelists but do no…
sit23 Jun 25, 2021
9bf3993
Remove simple cloud flag so trip tests will run
penmaher Jun 25, 2021
cb534b4
Adding more outputs.
sit23 Jun 25, 2021
77f2150
Removed flag entirely
penmaher Jun 25, 2021
7257b23
Adding namelist checking to idealized-moist-phys. This will raise an …
sit23 Jun 25, 2021
9f479c2
Problem is that sometimes check_nml_error is done for one method of r…
sit23 Jun 25, 2021
a8b886a
Adding namelist checking to case when using an internal-file-nml.
sit23 Jun 25, 2021
5e62d96
Added check-nml-error.
sit23 Jun 25, 2021
73e9d4d
Added check-nml-error.
sit23 Jun 25, 2021
f0de438
Added check-nml-error.
sit23 Jun 25, 2021
850b733
Added check-nml-error.
sit23 Jun 25, 2021
503e7f2
Added check-nml-error.
sit23 Jun 25, 2021
fe3a948
Added check-nml-error.
sit23 Jun 25, 2021
35ba489
Added check-nml-error.
sit23 Jun 25, 2021
bd86ce2
Added check-nml-error.
sit23 Jun 25, 2021
283d0de
Added check-nml-error.
sit23 Jun 25, 2021
3b170ce
Added check-nml-error.
sit23 Jun 25, 2021
669c366
Added extra comments for clarity.
sit23 Jun 25, 2021
01c382b
Change used from real to logical. Working through travis checks
penmaher Jun 28, 2021
d18aaa5
Merge pull request #213 from sit23/check_nml
sit23 Jun 28, 2021
1c42c8e
Reverted changes to RRTM back to the master. Shape (rank) mismatches …
penmaher Jun 28, 2021
95074a1
Reverted path names for RRTM back to master.
penmaher Jun 28, 2021
656a21e
Found part of cloud scheme without the do_simple_cloud flag. Attempte…
penmaher Jul 1, 2021
8c39828
Forgot to pass cloud logical flat back to interface. Will not compile…
penmaher Jul 1, 2021
803051d
Testing if nd_layer_clr is the case for difference in the trip test
penmaher Jul 1, 2021
35d666c
Not the case of the trip test fail
penmaher Jul 1, 2021
d69839e
Removed the four vars used in the simple cloud scheme to test if they…
penmaher Jul 2, 2021
a367654
Manually turned off all cloud related sections and vars
penmaher Jul 2, 2021
665d967
Removed more cloud vars
penmaher Jul 2, 2021
67d951e
Reverting to master version of this file. Still bug finding
penmaher Jul 2, 2021
9b7717b
Modified to allow release with current version of isca.
Jul 5, 2021
8a715ca
Merge pull request #198 from daw538/newdocs
daw538 Jul 5, 2021
0282f7b
Revert "Reverting to master version of this file. Still bug finding"
sit23 Jul 12, 2021
2d7ee52
Revert "Removed more cloud vars"
sit23 Jul 12, 2021
3e34a61
Revert "Manually turned off all cloud related sections and vars"
sit23 Jul 12, 2021
9f22399
Revert "Removed the four vars used in the simple cloud scheme to test…
sit23 Jul 12, 2021
949f1f0
Revert "Not the case of the trip test fail"
sit23 Jul 12, 2021
e70400c
Revert "Testing if nd_layer_clr is the case for difference in the tri…
sit23 Jul 12, 2021
f81a6bb
Adding functionality to check not only if code exists, but also if co…
sit23 Jul 12, 2021
eaa2dc3
Adding functionality to trip test that makes sure that the input name…
sit23 Jul 12, 2021
710a817
Merge pull request #208 from penmaher/simple_clouds
sit23 Jul 13, 2021
30a58f7
add docs github action
dennissergeev Jul 30, 2021
571a1e3
update docs workflow
dennissergeev Jul 30, 2021
75d120a
Merge pull request #1 from dennissergeev/gh_actions
dennissergeev Jul 30, 2021
8bf4a82
update docs environment
dennissergeev Jul 30, 2021
bf0b72f
fix the name of the branch in the docs workflow
dennissergeev Jul 30, 2021
ce1bbed
link the remote_access guide to docs
dennissergeev Jul 30, 2021
d5c84a8
update docs workflow
dennissergeev Jul 30, 2021
8d2bc8d
change env paths in the docs workflow
dennissergeev Jul 30, 2021
01641eb
test docs workflow
dennissergeev Jul 30, 2021
02f3dd5
test docs workflow
dennissergeev Jul 30, 2021
27aa1e2
test docs workflow
dennissergeev Jul 30, 2021
0e05d63
test docs workflow
dennissergeev Jul 30, 2021
37d969e
test docs workflow
dennissergeev Jul 30, 2021
10362f2
test docs workflow
dennissergeev Jul 30, 2021
a3622d9
add docs makefile
dennissergeev Jul 30, 2021
2e6ca1d
add tests workflow and switch to python 3.9
dennissergeev Jul 30, 2021
887b72d
rename conda environment in the tests workflow
dennissergeev Jul 30, 2021
1241df3
update tests workflow
dennissergeev Jul 30, 2021
7a39452
change GFDL_ paths in the tests workflow
dennissergeev Jul 30, 2021
a6170d3
update readme badges
dennissergeev Jul 30, 2021
a38349b
add citation file
dennissergeev Jul 30, 2021
41aadce
add gmd logo to readme
dennissergeev Jul 30, 2021
c83453b
move .travis.yml and other old files to the deprecated/ folder
dennissergeev Jul 30, 2021
c1e14e8
Merge pull request #216 from dennissergeev/master
dennissergeev Aug 2, 2021
f250c66
Edit Readme.md to refer to .yml file and recommend Miniforge'
Aug 23, 2021
dfa08ce
Fix typo, missing full stop
Aug 23, 2021
15bc373
Edits to ReadMe.md: Correct conda activate command; add miniforge rec…
Aug 23, 2021
af7a6ac
Enumerate steps as per Denis' suggestion
Aug 23, 2021
62a89c6
Fix formatting
Aug 23, 2021
ad27732
Fix formatting II
Aug 23, 2021
bf6a8b5
Italicise note on miniforge
Aug 23, 2021
c50316d
conda installed -> conda version installed
Aug 23, 2021
9694002
Add apostrophes
Aug 23, 2021
d8fb598
Allocation of v_10m was deleted during cleaning of initials from code…
Aug 26, 2021
4006f44
Merge pull request #220 from ExeClim/v_10m_bugfix
Aug 27, 2021
a06c2f6
Merge pull request #218 from RuthG/readme_edits
Aug 27, 2021
809b9a3
Axisymmetric test case crashes under gfortran. This is because the dt…
sit23 Aug 27, 2021
7dc6810
Identified cause of segmentation faults as loop with wrong dimensions.
sit23 Aug 27, 2021
b6731e5
Clearing up odd optional variables in rayleigh bottom drag.
sit23 Aug 27, 2021
fece063
Changing == to .eqv. for logicals, as gfortran objects to these even …
sit23 Aug 27, 2021
07472dd
Update to trip-tests to track when compilation rather than run fails.
sit23 Sep 23, 2021
4ae016f
Merge pull request #207 from RuthG/surface_flux_docs
Oct 7, 2021
575e8ea
Merge pull request #205 from rosscastle/begginers_guide
mckimb Oct 7, 2021
bf03df4
Update index.rst
rosscastle Oct 7, 2021
c7befa4
Merge branch 'master' into master_copy_mp_diagmanag_docs
rosscastle Oct 7, 2021
b7d50a3
Update index.rst
rosscastle Oct 7, 2021
403f230
Merge pull request #199 from mp586/master_copy_mp_diagmanag_docs
rosscastle Oct 7, 2021
6fd16c9
Create bve_swe_equations.rst
rosscastle Oct 7, 2021
87daf82
Update index.rst
rosscastle Oct 7, 2021
28f012c
Update index.rst
rosscastle Oct 13, 2021
5a69bd0
Create lscale_cond.rst
rosscastle Oct 13, 2021
9a70994
Update lscale_cond.rst
rosscastle Oct 13, 2021
9fb286e
Update lscale_cond.rst
rosscastle Oct 13, 2021
b5579eb
Update lscale_cond.rst
rosscastle Oct 13, 2021
3acc1db
Merge branch 'master' into shallow_and_baro_clean
sit23 Oct 16, 2021
6e259f5
Merge branch 'master' into gfortran_fixes
sit23 Oct 16, 2021
2f3b925
Merge branch 'gfortran_fixes' into shallow_and_baro_clean_gfort
sit23 Oct 16, 2021
e099244
Moving the cb.compile step inside the main executable part of the tes…
sit23 Oct 16, 2021
a9610f5
Adding shallow water and barotropic vorticity equation test cases to …
sit23 Oct 16, 2021
a8798e7
Last minor changes
rosscastle Oct 25, 2021
becb85c
Merge branch 'master' into isca_docs
rosscastle Oct 25, 2021
cbfb749
Merge pull request #172 from rosscastle/isca_docs
matthewjhenry Oct 25, 2021
85d6425
Merge branch 'master' into topog_docs
rosscastle Oct 25, 2021
9615f09
MP Changes
rosscastle Oct 25, 2021
04e8539
Update references.rst
rosscastle Oct 25, 2021
d4c8256
adding initial code to allow an initial condition for h, vor and div …
sit23 Oct 26, 2021
1a226ec
Updated cftime calls to interface with latest version.
sit23 Oct 27, 2021
398a8df
Adding option to create timeseries file without time variation, and w…
sit23 Oct 27, 2021
9044fbb
When defining the h field in the input file, take the convention that…
sit23 Oct 27, 2021
d4b1529
Add script to create sw initial conditions, initially following the R…
sit23 Oct 27, 2021
deb2181
Adding test case for shallow water with prescribed initial conditions…
sit23 Oct 27, 2021
23cc2b6
Adding references and general planet radius to init cond script.
sit23 Oct 27, 2021
72c7219
Updated windspharm call to note that this is latitude on a gaussian g…
sit23 Oct 28, 2021
e1a1033
Ruth Comments
rosscastle Nov 1, 2021
5842293
Merge pull request #222 from sit23/gfortran_fixes
sit23 Nov 3, 2021
1d42e82
Include RuthG
matthewjhenry Mar 24, 2022
4129f51
Merge branch 'master' into doc_mixedlayer
matthewjhenry Mar 24, 2022
623dc2f
Merge pull request #188 from matthewjhenry/doc_mixedlayer
matthewjhenry Mar 24, 2022
737e2ea
Merge pull request #224 from rosscastle/bve_swe_docs
May 25, 2022
bae8e32
Update lscale_cond.rst
May 25, 2022
2f29f69
Merge pull request #196 from rosscastle/topog_docs
May 25, 2022
5ae1ca6
Merge branch 'master' into scale_docs
May 25, 2022
e11f5ed
Merge pull request #226 from rosscastle/scale_docs
May 25, 2022
ce47380
Update mkmf file to fix gfotran compile issue
ntlewis May 30, 2022
db1acfb
Update mkmf.template.ubuntu_conda
ntlewis May 30, 2022
2b77038
actually fix syntax issue
ntlewis May 30, 2022
24c47d0
Merge branch 'master' into column_model_pr
ntlewis May 31, 2022
8f57162
add other compiler flag stephen suggested
ntlewis Jun 8, 2022
5f773e3
syntax again
ntlewis Jun 8, 2022
075148e
syntax again
ntlewis Jun 8, 2022
3aa554c
syntax hopefull done now
ntlewis Jun 8, 2022
9560521
Merge pull request #236 from ntlewis/fix_boz_compile_error
ntlewis Jun 8, 2022
d267f91
Merge branch 'master' into column_model_pr
ntlewis Jun 8, 2022
577db78
update column path names to include simple cloud scheme
ntlewis Jun 8, 2022
607eaac
Updated @qlxyz simple_clouds branch with latest master.
Feb 28, 2023
2a835de
Fixed duplicate assignment that was preventing compilation
Feb 28, 2023
19c4431
Reverting RRTM+cloud merger to test as failing compilation
Feb 28, 2023
424871f
More debugging to run trip tests
Feb 28, 2023
88db95d
Further compilation fixes
Mar 4, 2023
6e2aa80
Re-enabled ice_concentration_threshold parameter to prevent realistic…
Mar 4, 2023
193e7f0
Testing differences in ice-albedo calculation
Mar 4, 2023
955df7f
Reinstate socrates+spookie cloud test cases
Mar 9, 2023
ce22384
Reintroducing spookie cloud model as separate to simcloud scheme
Mar 9, 2023
a26b31d
Renaming cloud_spookie diag name to try to fix trip test failure
Mar 9, 2023
a556a6b
Introduced option to switch method used to calculate albedo in presen…
Mar 9, 2023
386ec8a
Added diagnostic messages to output to show cloud scheme in use. Adde…
Mar 15, 2023
3d506c8
Allowing both SimCloud and SPOOKIE to be passed to SOCRATES
Mar 16, 2023
c68238b
Update existing socrates test cases for consistency
Mar 16, 2023
9e78f16
First working compile of Isca on maths2 using locally installed intel…
sit23 Mar 16, 2023
d4ddecb
Removing files that should not be in PR
May 4, 2023
9603436
Removing personalised comments and tidying terminology
May 4, 2023
abc8fcb
Further comment tidying
May 4, 2023
d3adefb
Fix a few typos in docs
pitmonticone May 5, 2023
3448e89
Small mod for sorting sh issue.
sit23 Jul 25, 2023
c233c04
Merge branch 'maths2intel' into sh_fix
sit23 Jul 25, 2023
4b38144
Created function that takes in the output of sh commands and checks i…
sit23 Jul 25, 2023
e5c5b20
Removing specific mentions of my directories.
sit23 Jul 25, 2023
d8a9bca
Merge branch 'sh_fix' into shallow_and_baro_clean_gfort_input_file
sit23 Jul 25, 2023
91f1555
Fixed bug in sh fix for writing out the git commit ID.
sit23 Oct 18, 2023
3c63ca3
Github actions seems to have problems with sh.cd, but on closer inspe…
sit23 Oct 18, 2023
5b72697
Merge pull request #255 from sit23/sh_fix
sit23 Oct 19, 2023
c067351
Reinstate spookie cloud test case
Oct 26, 2023
5f9daa3
Merge remote-tracking branch 'upstream/master' into simcloud
Oct 26, 2023
ea22d13
Fixes for gfortran compilation
Oct 26, 2023
1feab10
Further fixes for gfortran compilation
Oct 26, 2023
7acc5d2
Merge pull request #246 from daw538/simcloud
daw538 Oct 26, 2023
6f96693
Updating environment file to only use openmpi v4 as recently released…
sit23 Jan 24, 2024
b64a423
Renamed env file as no longer specific to python 3.9.
sit23 Jan 24, 2024
2d15c9b
Adding version of environment file with package versions that we have…
sit23 Jan 24, 2024
63d8bd8
Updating the test suite to use the frozen version of the env file.
sit23 Jan 24, 2024
27e35a6
Fixing typo in frozen env file with dask version. Updating Readme to …
sit23 Jan 24, 2024
4c89e9d
Merge pull request #249 from pitmonticone/master
sit23 Jan 24, 2024
c045b00
Merge pull request #260 from sit23/env_freeze
ntlewis Jan 25, 2024
6350a46
add flag to constrain q to be decreasing with height only
ntlewis Feb 26, 2024
0249cac
add code to use lcl depth for pbl depth
ntlewis Feb 26, 2024
eb7fa09
fix additions for lcl bl depth and stratospheric q
ntlewis Feb 27, 2024
a463bbe
Merge branch 'master' into column_model_pr
ntlewis Feb 28, 2024
d055759
re-add ability to prescribe ozone in SCM
ntlewis Feb 28, 2024
ea1833f
add simple cloud scheme path names
ntlewis Feb 28, 2024
bd28843
Update path_names
ntlewis Feb 28, 2024
cccc6f4
Update path_names to include socrates_set_cld
ntlewis Feb 28, 2024
ef5ad18
fix if statement .eqv. in socrates_interface (bug introduced when clo…
ntlewis Feb 28, 2024
92da4a8
fix python scm_interp_routine used to compute ozone profile for SCM
ntlewis Feb 28, 2024
0886ff6
increase run length for default column_test
ntlewis Feb 28, 2024
21d348a
specify bind-to socket when running SCM experiments (this means that …
ntlewis Feb 28, 2024
bf8fe9d
turn on Brett's options to constrain stratospheric q, and to use the …
ntlewis Feb 28, 2024
8556034
change initial specific humidity to q=1e-3, so that stratospheric q i…
ntlewis Feb 28, 2024
c62e1a6
tidy comments
ntlewis Feb 28, 2024
123c5c2
Update test_cases README.md to mention SCM
ntlewis Feb 28, 2024
dd8d134
modify ape_aquaplanet experiment so that it runs with gfortran (conve…
ntlewis Feb 29, 2024
7f335ed
Delete src/extra/env/ox-desk2
ntlewis Feb 29, 2024
f4a950d
Update column_test.py
ntlewis Feb 29, 2024
2dd2005
Update column_test_rrtm_ozone.py
ntlewis Feb 29, 2024
4389661
Update column_test_socrates_ozone.py
ntlewis Feb 29, 2024
dbaa8c1
Update column_test.py
ntlewis Feb 29, 2024
8cf7d60
Delete src/extra/python/isca/templates/mkmf.template.ox
ntlewis Feb 29, 2024
f77ba4e
Merge pull request #82 from ntlewis/column_model_pr
ntlewis Mar 4, 2024
e601caa
Merge branch 'master' into shallow_and_baro_clean_gfort_input_file
sit23 Aug 5, 2024
8e45135
Merge pull request #268 from sit23/shallow_and_baro_clean_gfort_input…
sit23 Aug 5, 2024
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65 changes: 65 additions & 0 deletions .github/ISSUE_TEMPLATE/bug_report.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,65 @@
---
name: Bug report
about: Use this template for submitting bug reports.
title: "[ISSUE TITLE]"
labels: bug
assignees:
---

<!--
Thank you for taking the time to create an issue for your topic/question.
This issue provides a permanent record for others with similar questions
to gain insight at a later date - your contributions here are significant
to the community and much appreciated!

Please always remember to be courteous to others posting on this forum as
we are all here voluntarily to help others use Isca.

NOTE:
Isca team members are all full-time research scientists, so while we are very happy to provide
some support, response times may vary. If you need in-depth support, then we may suggest that one
of us becomes a co-author on your next paper by providing long-term support on the issue.
-->

<!--
Please be sure to add an informative title to this issue
-->

## Description
<!--
Fill out a concise description of your topic/question in this section.
Feel free to post your code here using Markdown formatting
-->

-----
**Screenshots**
<!--
If applicable, add screenshots to help explain your problem.
-->

-----
**Isca version**
<!--
Please provide here your recent commit ID and tell us if you are working off your own fork or just
using the main Execlim verion.
-->

-----
**System Information:**
To help us track down bugs faster, please provide the details about the machine where you run Isca.

To do this, run the following code in Python:
```py
import platform
print(platform.uname())
```
and paste the output below.
```txt
# Paste system info here

```
-----
## Minimal reproducible example
<!--
It greatly helps us address your question if you have example data or script for us to work with.
-->
33 changes: 33 additions & 0 deletions .github/ISSUE_TEMPLATE/docs_issue.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,33 @@
---
name: Documentation issue
about: Use this template for submitting documentation-related issues.
title: "[ISSUE TITLE]"
labels: docs
assignees:
---

<!--
Thank you for taking the time to create an issue for your topic/question.
This issue provides a permanent record for others with similar questions
to gain insight at a later date - your contributions here are significant
to the community and much appreciated!

Please always remember to be courteous to others posting on this forum as
we are all here voluntarily to help others use Isca.

NOTE:
Isca team members are all full-time research scientists, so while we are very happy to provide
some support, response times may vary. If you need in-depth support, then we may suggest that one
of us becomes a co-author on your next paper by providing long-term support on the issue.
-->

<!--
Please be sure to add an informative title to this issue
-->

## Description
<!--
Fill out a concise description of your topic/question in this section.
Feel free to post your code here using Markdown formatting
-->

23 changes: 23 additions & 0 deletions .github/ISSUE_TEMPLATE/feature_request.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
---
name: Feature Request
about: Suggest an idea for something new to add
labels:
---
<!--
Thank you for taking the time to create an issue for your topic/question.
This issue provides a permanent record for others with similar questions
to gain insight at a later date - your contributions here are significant
to the community and much appreciated!

Please always remember to be courteous to others posting on this forum as
we are all here voluntarily to help others use Isca.

NOTE:
Isca team members are all full-time research scientists, so while we are very happy to provide
some support, response times may vary. If you need in-depth support, then we may suggest that one
of us becomes a co-author on your next paper by providing long-term support on the issue.
-->
## Description
<!--
Include a clear description and an example or even a scholarly source of information about the feature.
-->
60 changes: 60 additions & 0 deletions .github/ISSUE_TEMPLATE/installation_issue.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,60 @@
---
name: Installation issue
about: Use this template if you have an issue related to installing Isca.
title: "[YOUR QUESTION]"
labels: infrastructure
assignees:
---

<!--
Thank you for taking the time to create an issue for your topic/question.
This issue provides a permanent record for others with similar questions
to gain insight at a later date - your contributions here are significant
to the community and much appreciated!

Please always remember to be courteous to others posting on this forum as
we are all here voluntarily to help others use Isca.

NOTE:
Isca team members are all full-time research scientists, so while we are very happy to provide
some support, response times may vary. If you need in-depth support, then we may suggest that one
of us becomes a co-author on your next paper by providing long-term support on the issue.
-->

<!--
Please be sure to add an informative title to this issue
-->

## Description
<!--
Fill out a concise description of your topic/question in this section.
Feel free to post your code here using Markdown formatting
-->

-----
**Screenshots**
<!--
If applicable, add screenshots to help explain your problem.
-->

-----
**Isca version**
<!--
Please provide here your recent commit ID and tell us if you are working off your own fork or just
using the main Execlim verion.
-->

-----
**System Information:**
To help us help you, provide the details about the machine where you are trying to install Isca.

To do this, please run the following code in Python:
```py
import platform
print(platform.uname())
```
and paste the output below.
```txt
# Paste system info here

```
42 changes: 42 additions & 0 deletions .github/ISSUE_TEMPLATE/science_issue.md
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@@ -0,0 +1,42 @@
---
name: Science issue
about: Use this template for submitting science-related issues.
title: "[YOUR QUESTION]"
labels:
assignees:
---

<!--
Thank you for taking the time to create an issue for your topic/question.
This issue provides a permanent record for others with similar questions
to gain insight at a later date - your contributions here are significant
to the community and much appreciated!

Please always remember to be courteous to others posting on this forum as
we are all here voluntarily to help others use Isca.

NOTE:
Isca team members are all full-time research scientists, so while we are very happy to provide
some support, response times may vary. If you need in-depth support, then we may suggest that one
of us becomes a co-author on your next paper by providing long-term support on the issue.
-->

<!--
Please be sure to add an informative title to this issue
-->

## Description
<!--
Fill out a concise description of your topic/question in this section.
Feel free to post your code here using Markdown formatting
-->

### Screenshots
<!--
If applicable, add screenshots to help explain your problem.
-->

## Minimal reproducible example
<!--
It greatly helps us address your question if you have example data or script for us to work with.
-->
85 changes: 85 additions & 0 deletions .github/workflows/docs.yml
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name: docs

on:
push:
branches: [ master ]
paths:
- '.github/workflows/docs.yml'
- 'docs/**'
- 'src/**'

env:
GFDL_BASE: ${{ github.workspace }}
GFDL_ENV: "ubuntu_conda"
GFDL_WORK: "$HOME/gfdl_work"
GFDL_DATA: "$HOME/gfdl_data"
GFDL_PYDIR: "${{ github.workspace }}/src/extra/python"

jobs:
docs:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest]
python-version: ['3.9']

steps:
- name: Checkout source
uses: actions/checkout@v2
with:
fetch-depth: 0

# - name: Check environment variables
# run: |
# echo "Testing"
# echo $PWD
# echo $GFDL_BASE
# echo $GFDL_PYDIR
# echo $GITHUB_WORKSPACE
# echo $GITHUB_SERVER_URL/$GITHUB_REPOSITORY/actions/runs/$GITHUB_RUN_ID

- name: Setup Conda Environment
uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: docs/environment.yml
miniforge-variant: Mambaforge
miniforge-version: "latest"
use-mamba: true
activate-environment: isca_docs
auto-activate-base: false

- name: List installed packages
shell: bash -l {0}
run: conda list

- name: Install
shell: bash -l {0}
run: |
cd $GFDL_PYDIR
python -m pip install -e .
cd $GFDL_BASE

- name: Build docs
shell: bash -l {0}
run: |
cd docs/
make html -e

- name: Commit documentation changes
run: |
git clone https://github.com/$GITHUB_REPOSITORY.git --branch gh-pages --single-branch gh-pages
cp -r docs/_build/html/* gh-pages/
cd gh-pages
git config --local user.email "action@github.com"
git config --local user.name "GitHub Action"
git add .
git commit -m "Update documentation" -a || true
# The above command will fail if no changes were present, so we ignore that.

- name: Push changes
uses: ad-m/github-push-action@master
with:
branch: gh-pages
directory: gh-pages
github_token: ${{ secrets.GITHUB_TOKEN }}
70 changes: 70 additions & 0 deletions .github/workflows/tests.yml
Original file line number Diff line number Diff line change
@@ -0,0 +1,70 @@
name: tests

on:
push:
branches: [ master ]
paths:
- '.github/workflows/tests.yml'
- 'bin/**'
- 'bin/**'
- 'ci/**'
- 'exp/**'
- 'input/**'
- 'src/**'
- 'test/**'
pull_request:
branches: [ master ]
paths:
- '.github/workflows/tests.yml'
- 'bin/**'
- 'ci/**'
- 'exp/**'
- 'input/**'
- 'src/**'
- 'test/**'

env:
GFDL_BASE: ${{ github.workspace }}
GFDL_ENV: "ubuntu_conda"
GFDL_WORK: "${{ github.workspace }}/../gfdl_work"
GFDL_DATA: "${{ github.workspace }}/../gfdl_data"
GFDL_PYDIR: "${{ github.workspace }}/src/extra/python"

jobs:
test:
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: [ubuntu-latest] # , macos-latest]
python-version: ['3.12']

steps:
- name: Checkout source
uses: actions/checkout@v2

- name: Setup Conda for OS ${{ matrix.os }} and Python ${{ matrix.python-version }}
uses: conda-incubator/setup-miniconda@v2
with:
python-version: ${{ matrix.python-version }}
environment-file: ci/environment-py${{ matrix.python-version }}_frozen.yml
miniforge-variant: Mambaforge
miniforge-version: "latest"
use-mamba: true
activate-environment: isca_env
auto-activate-base: false

- name: Install
shell: bash -l {0}
run: |
cd $GFDL_PYDIR
python -m pip install -e .
cd $GFDL_BASE

- name: List installed packages
shell: bash -l {0}
run: conda list

- name: Run tests
shell: bash -l {0}
run: |
python -m pytest
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