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Fixed bug in HRefODrag; Updated Actions yaml files #293

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merged 25 commits into from
Aug 16, 2024
Merged

Fixed bug in HRefODrag; Updated Actions yaml files #293

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e16b93e
Updated some unit tests that I missed last time.
Apr 22, 2024
537b1ec
Changed logic in unit test yamls to improve reliability of unit test …
Apr 22, 2024
73e9a13
Added sudo apt-get update to workflow yamls.
Apr 22, 2024
5fb6590
Updated workflow ymls to update apt-get, if applicable.
RoryBarnes Apr 23, 2024
4423e7a
Removed potential div-by-zero calculations in atmesc.c
RoryBarnes Apr 23, 2024
2c0880b
Printing output from an error running vplanet now.
Apr 23, 2024
7e5d898
Moved error message in wrapper.py
Apr 23, 2024
6cb2379
Began removing sprintf...
RoryBarnes Apr 24, 2024
df2383f
Merge branch 'HRefODrag' of https://github.com/VirtualPlanetaryLabora…
RoryBarnes Apr 24, 2024
c06c139
Changed error message in wrapper.py to actually report the error.
Apr 25, 2024
1ce0e74
Merge branch 'HRefODrag' of https://github.com/VirtualPlanetaryLabora…
Apr 25, 2024
dd706bc
Removed all instances of sprintf. Code untested.
Apr 26, 2024
939f20a
Updated string copies to use fvFormattedString.
May 23, 2024
b24fe70
Recasted a few more string arrays to pointers to work with new Format…
Jul 25, 2024
e039aa0
Updated ReadOption functions to work with new FormattedString function.
Aug 1, 2024
31e2e24
More updates to string formatting.
Aug 3, 2024
33272aa
Finished removing all instances of stcpy, strcat, and sprintf. Code c…
Aug 6, 2024
ee7581b
Merge branch 'main' of https://github.com/VirtualPlanetaryLaboratory/…
Aug 6, 2024
9bee7c9
Working to solve issue with assignment of string arrays...
Aug 6, 2024
49bd690
Refactored InitializeControl and added new funciton InitializeFiles. …
RoryBarnes Aug 7, 2024
04465da
Code now compiles and one test simulation passes!
Aug 8, 2024
dcf761f
More fixes, but tests are still erroring or failing.
Aug 8, 2024
c15999e
Added checks for when the oxygen mixing ratio is 1. If it is than HRe…
Aug 9, 2024
74609fc
Most string issues found. All the tests pass some of the time. Next u…
Aug 9, 2024
4a1f984
Refactoring ReadInitialOptions...
RoryBarnes Aug 13, 2024
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1 change: 1 addition & 0 deletions .github/workflows/docs.yml
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Expand Up @@ -24,6 +24,7 @@ jobs:
if: steps.setup_python.outcome == 'success'
shell: bash -l {0}
run: |
sudo apt-get update
sudo apt-get install -y doxygen
sudo apt-get install -y doxygen-doc
python -m pip install -U pip
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1 change: 0 additions & 1 deletion .github/workflows/examples.yml
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Expand Up @@ -26,7 +26,6 @@ jobs:
sudo apt-get install cm-super
sudo apt-get install texlive-fonts-recommended texlive-fonts-extra
sudo apt-get install dvipng
sudo apt-get update

- name: Set up Python
id: setup_python
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1 change: 1 addition & 0 deletions .github/workflows/memcheck.yml
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Expand Up @@ -29,6 +29,7 @@ jobs:
if: steps.setup_python.outcome == 'success'
shell: bash -l {0}
run: |
sudo apt-get update
sudo apt-get install valgrind

- name: Run valgrind test
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13 changes: 11 additions & 2 deletions .github/workflows/tests-linux.yml
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Expand Up @@ -34,15 +34,19 @@ jobs:
if: steps.setup_python.outcome == 'success'
shell: bash -l {0}
run: |
sudo apt-get update
python -m pip install -U pip
python -m pip install -e .
pip install pytest pytest-cov
sudo apt install lcov

- name: Run tests and generate coverage
- name: Run tests
id: test
if: steps.install.outcome == 'success'
shell: bash -l {0}
run: make coverage
run: |
make opt
pytest --tb=short

- name: Check test ouptut created
id: check_test_file
Expand All @@ -51,6 +55,11 @@ jobs:
files: "/home/runner/work/vplanet/vplanet/junit/test-results.xml"
fail: true

- name: Generate coverage
id: coverage
if: steps.test.outcome == 'success' && steps.check_test_file.outcome == 'success'
run: make coverage

- name: Get unique id
uses: Tiryoh/gha-jobid-action@v1
id: jobs
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4 changes: 3 additions & 1 deletion .github/workflows/tests-macos-intel.yml
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Expand Up @@ -33,7 +33,9 @@ jobs:

- name: Run tests
if: steps.setup_python.outcome == 'success'
run: make test
run: |
make opt
pytest --tb=short

- name: Get unique id
uses: Tiryoh/gha-jobid-action@v1
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2 changes: 1 addition & 1 deletion .github/workflows/tests-macos-silicon.yml
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Expand Up @@ -35,7 +35,7 @@ jobs:
if: steps.setup_python.outcome == 'success'
run: |
make opt
pytest
pytest --tb=short

- name: Get unique id
uses: Tiryoh/gha-jobid-action@v1
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544 changes: 275 additions & 269 deletions src/atmesc.c
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24 changes: 12 additions & 12 deletions src/atmesc.h
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Expand Up @@ -177,29 +177,29 @@ void InitializeOutputFunctionAtmEsc(OUTPUT *, int, int);
void FinalizeOutputFunctionAtmEsc(OUTPUT *, int, int);

void WriteSurfaceWaterMass(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *,
UPDATE *, int, double *, char[]);
UPDATE *, int, double *, char**);
void WriteOxygenMass(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *, UPDATE *,
int, double *, char[]);
int, double *, char**);
void WriteOxygenMantleMass(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *,
UPDATE *, int, double *, char[]);
UPDATE *, int, double *, char**);
void WriteEnvelopeMass(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *, UPDATE *,
int, double *, char[]);
int, double *, char**);
void WriteRGLimit(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *, UPDATE *, int,
double *, char[]);
double *, char**);
void WriteBondiRadius(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *, UPDATE *,
int, double *, char[]);
int, double *, char**);
void WriteRocheRadius(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *, UPDATE *,
int, double *, char[]);
int, double *, char**);
void WriteOxygenMixingRatio(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *,
UPDATE *, int, double *, char[]);
UPDATE *, int, double *, char**);
void WriteOxygenEta(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *, UPDATE *,
int, double *, char[]);
int, double *, char**);
void WriteAtmXAbsEffH2O(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *,
UPDATE *, int, double *, char[]);
UPDATE *, int, double *, char**);
void WriteRRCriticalFlux(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *,
UPDATE *, int, double *, char[]);
UPDATE *, int, double *, char**);
void WriteHEscapeRegime(BODY *, CONTROL *, OUTPUT *, SYSTEM *, UNITS *,
UPDATE *, int, double *, char[]);
UPDATE *, int, double *, char**);

/* Logging Functions */
void LogOptionsAtmEsc(CONTROL *, FILE *);
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