Merge pull request #252 from VirtualPlanetaryLaboratory/os-tests

Added workflows to test Linux and Mac builds. Windows users will have to use the Windows Subsystem for Linux: https://learn.microsoft.com/en-us/windows/wsl/install. The code is now checked on Ubuntu 20.04 and 22.04, MacOS 11, 12 and 13.
VirtualPlanetaryLaboratory · Nov 1, 2023 · a239fb8 · a239fb8
2 parents ef85dbf + 161ff39
commit a239fb8
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Showing 9 changed files with 145 additions and 128 deletions.
diff --git a/.github/workflows/pip-install.yml b/.github/workflows/pip-install.yml
@@ -10,7 +10,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest]
         python: ['3.7', '3.8', '3.9', '3.10', '3.11']
     steps:
       - uses: actions/checkout@v3

diff --git a/.github/workflows/tests.yml → .github/workflows/tests-linux.yml b/.github/workflows/tests.yml → .github/workflows/tests-linux.yml
@@ -1,26 +1,24 @@
-name: tests
+name: tests-linux
 
 on:
   push:
-    branches: [master, main]
+    branches: [main]
   pull_request:
-    branches: [master, main]
+    branches: [main]
   workflow_dispatch:
 
 jobs:
   tests:
-    name: 'Run tests on py${{ matrix.python-version }}'
-    runs-on: ubuntu-latest
+    name: '${{ matrix.os }}:python-${{ matrix.python-version }}'
+    runs-on: ${{ matrix.os }}
     strategy:
-      fail-fast: false
       matrix:
-        include:
-          - python-version: '3.6'
-          - python-version: '3.7'
-          - python-version: '3.8'
-          - python-version: '3.9'
-          - python-version: '3.10'
-          - python-version: '3.11'
+        os: [ubuntu-20.04, ubuntu-22.04]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11']
+        exclude:
+          - os: ubuntu-22.04
+            python-version: '3.6'
+      fail-fast: false
 
     steps:
       - uses: actions/checkout@v3
@@ -29,10 +27,8 @@ jobs:
 
       - name: Set up Python
         id: setup_python
-        uses: conda-incubator/setup-miniconda@v2
+        uses: actions/setup-python@v4
         with:
-          activate-environment: vplanet
-          environment-file: environment.yml
           python-version: ${{ matrix.python-version }}
 
       - name: Install
@@ -42,30 +38,32 @@ jobs:
         run: |
           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
         if: steps.install.outcome == 'success'
         shell: bash -l {0}
-        run: |
-          make coverage
+        run: make coverage
+
+      - name: Check test ouptut created
+        id: check_test_file
+        uses: andstor/file-existence-action@v2
+        with:
+          files: "/home/runner/work/vplanet/vplanet/junit/test-results.xml"
+          fail: true
 
       - name: Get unique id
-        id: unique-id
-        env:
-          STRATEGY_CONTEXT: ${{ toJson(strategy) }}
-        run: |
-          export JOB_ID=`echo $STRATEGY_CONTEXT | md5sum`
-          echo "::set-output name=id::$JOB_ID"
+        uses: Tiryoh/gha-jobid-action@v1
+        id: jobs
 
       - name: Publish unit test results
-        uses: EnricoMi/publish-unit-test-result-action@v1
+        uses: EnricoMi/publish-unit-test-result-action@v2
         if: always()
         with:
           files: junit/test-*.xml
-          comment_mode: update last
 
       - name: CodeCov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3
         with:
           files: ./.coverage
diff --git a/.github/workflows/tests-macos.yml b/.github/workflows/tests-macos.yml
@@ -0,0 +1,55 @@
+name: tests-macos
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+jobs:
+  tests:
+    name: '${{ matrix.os }}:python-${{ matrix.python-version }}'
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [macos-11, macos-12, macos-13]
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10', '3.11', '3.12']
+      fail-fast: false
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        id: setup_python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        if: steps.setup_python.outcome == 'success'
+        run: |
+          python -m pip install -U pip
+          python -m pip install -e .
+          python -m pip install pytest pytest-cov
+
+      - name: Run tests
+        if: steps.setup_python.outcome == 'success'
+        run: make test
+
+      - name: Check test ouptut created
+        id: check_test_file
+        uses: andstor/file-existence-action@v2
+        with:
+          files: "/home/runner/work/vplanet/vplanet/junit/test-results.xml"
+          fail: true
+
+      - name: Get unique id
+        uses: Tiryoh/gha-jobid-action@v1
+        id: jobs
+
+      - name: Publish unit test results
+        uses: EnricoMi/publish-unit-test-result-action/composite@v2
+        if: always()
+        with:
+          files: junit/test-*.xml
diff --git a/README.md b/README.md
@@ -5,32 +5,60 @@
 <h1 align="center">VPLanet: The Virtual Planet Simulator</h1>
 
 <p align="center">
-  <a href="https://VirtualPlanetaryLaboratory.github.io/vplanet"><img src="https://img.shields.io/badge/Read-the_docs-blue.svg?style=flat"></a>
+  <a href="https://VirtualPlanetaryLaboratory.github.io/vplanet">
+    <img src="https://img.shields.io/badge/Read-the_docs-blue.svg?style=flat">
+  </a>
   <a href="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/docs.yml">
-  <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/docs.yml/badge.svg"></a>
-  <a href="https://ui.adsabs.harvard.edu/abs/2019arXiv190506367B/abstract"><img src="https://img.shields.io/badge/Read-the_paper-darkgreen.svg?style=flat"></a>
-  <a href="https://VirtualPlanetaryLaboratory.github.io/vplanet/conduct.html"><img src="https://img.shields.io/badge/Code%20of-Conduct-7d93c7.svg"></a>
-  <a href="https://www.youtube.com/@VPLanetCode/playlists"><img src="https://img.shields.io/badge/You-Tube-darkred.svg"></a><br>
-  <img src="https://img.shields.io/badge/Unit%20Tests-14,440-darkblue.svg"></a>
-  <a href="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests.yml">
-  <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests.yml/badge.svg"></a>
-  <img src="https://img.shields.io/badge/Memory%20Checks-43-darkblue.svg"></a>
+    <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/docs.yml/badge.svg">
+  </a>
+  <a href="https://ui.adsabs.harvard.edu/abs/2019arXiv190506367B/abstract">
+    <img src="https://img.shields.io/badge/Read-the_paper-darkgreen.svg?style=flat">
+  </a>
+  <a href="https://VirtualPlanetaryLaboratory.github.io/vplanet/conduct.html">
+    <img src="https://img.shields.io/badge/Code%20of-Conduct-7d93c7.svg">
+  </a>
+  <a href="https://www.youtube.com/@VPLanetCode/playlists">
+    <img src="https://img.shields.io/badge/You-Tube-darkred.svg">
+  </a>
+  <br>
+  <img src="https://img.shields.io/badge/Unit%20Tests-14,440-darkblue.svg">
+  <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests-linux.yml/badge.svg">
+  <img src="https://img.shields.io/badge/Ubuntu%2020-Python%203.6%20--%203.11-7d93c7.svg">
+  <img src="https://img.shields.io/badge/Ubuntu%2022-Python%203.7%20--%203.11-7d93c7.svg">
+  <br>
+  <a href="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests-macos.yml">
+    <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/tests-macos.yml/badge.svg">
+  </a>
+  <img src="https://img.shields.io/badge/Mac%20OS11-Python%203.6%20--%203.11-7d93c7.svg">
+  <img src="https://img.shields.io/badge/Mac%20OS12-Python%203.6%20--%203.11-7d93c7.svg">
+  <img src="https://img.shields.io/badge/Mac%20OS13-Python%203.6%20--%203.11-7d93c7.svg">
+  <br>
+  <img src="https://img.shields.io/badge/Memory%20Checks-43-darkblue.svg">
   <a href="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/memcheck.yml">
-  <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/memcheck.yml/badge.svg"></a>
+    <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/memcheck.yml/badge.svg">
+  </a>
   <a href="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet">
-  <img src="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet/branch/master/graph/badge.svg?token=3LFJQO1M6H"><br>
-  <a href="examples"><img src="https://img.shields.io/badge/Examples-42-darkblue.svg"></a>
+    <img src="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet/branch/main/graph/badge.svg?token=3LFJQO1M6H">
+  </a>
+  <br>
+  <a href="examples">
+    <img src="https://img.shields.io/badge/Examples-42-darkblue.svg">
+  </a>
   <a href="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/examples.yml">
-  <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/examples.yml/badge.svg"></a>
-  <img src="https://img.shields.io/badge/Python-3.6%20--%203.11-7d93c7.svg"></a>
+    <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/examples.yml/badge.svg">
+  </a>
+  <img src="https://img.shields.io/badge/Python-3.6%20--%203.11-7d93c7.svg">
   <a href="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/pip-install.yml">
-  <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/pip-install.yml/badge.svg"></a><br>
-  <img src = "https://img.shields.io/badge/Platforms-Linux_|%20macOS_|%20Windows10-darkgreen.svg?style=flat">
-  <a href="http://ascl.net/1811.017"><img src="https://img.shields.io/badge/ASCL-1811.017-orange.svg?colorB=orange" alt="ascl:1811.017" /></a>
-  <a href="https://emac.gsfc.nasa.gov"><img src="https://img.shields.io/badge/EMAC-2207%E2%80%94138-blue.svg"></a>
-  <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-purple.svg"/></a><br>
-
-
+    <img src="https://github.com/VirtualPlanetaryLaboratory/vplanet/actions/workflows/pip-install.yml/badge.svg">
+  </a>
+  <br>
+  <a href="http://ascl.net/1811.017">
+    <img src="https://img.shields.io/badge/ASCL-1811.017-orange.svg?colorB=orange" alt="ascl:1811.017">
+  </a>
+  <a href="https://emac.gsfc.nasa.gov">
+    <img src="https://img.shields.io/badge/EMAC-2207%E2%80%94138-blue.svg">
+  </a>
+    <a href="LICENSE"><img src="https://img.shields.io/badge/License-MIT-purple.svg"/>
   </a>
 </p>
 
@@ -83,11 +111,11 @@ Many of these modules can be combined together to simulate numerous phenomena an
 
 The [examples/](examples) directory contains input files and scripts for generating the figures in [Barnes et al. (2020)](https://ui.adsabs.harvard.edu/abs/2020PASP..132b4502B/abstract) and subsequent publications. The "examples" badge shows if all the examples can be built with the most recent version. The [Manual/](Manual) directory contains the pdf of [Barnes et al. (2020)](https://ui.adsabs.harvard.edu/abs/2020PASP..132b4502B/abstract), which describes the physics of the first 11 modules, validates the software against observations and/or past results, and uses figures from the [examples/](examples) directory.
 
-An ecosystem of support software is also publicly available. [VPLot](https://github.com/VirtualPlanetaryLaboratory/vplot) is both a command line tool to quickly plot the evolution of a single integration, and also includes matplotlib functions to generate publication-worthy figures. The [VSPACE](https://github.com/VirtualPlanetaryLaboratory/vspace) script generates input files for a parameter space sweep, which can then be performed on an arbitrary number of cores with [MultiPlanet](https://github.com/VirtualPlanetaryLaboratory/multi-planet). For large parameter sweeps, an enormous amount of data can be generated, which can slow analyses. To overcome this barrier, the [BigPlanet](https://github.com/VirtualPlanetaryLaboratory/bigplanet) code can both compress datasets into HDF5 format, including statistics of an integration, and tools to facilitate plotting. These three scripts can be executed from the command line to seamlessly [perform parameter sweeps](https://virtualplanetarylaboratory.github.io/vplanet/parametersweep.html). These Python scripts are optimized for [anaconda](https://www.anaconda.com/) distributions versions 3.5-3.9. The "wheels" badge indicates if you can download and install the executables with pip for these Python distributions.
+An ecosystem of support software is also publicly available. [VPLot](https://github.com/VirtualPlanetaryLaboratory/vplot) is both a command line tool to quickly plot the evolution of a single integration, and also includes matplotlib functions to generate publication-worthy figures. The [VSPACE](https://github.com/VirtualPlanetaryLaboratory/vspace) script generates input files for a parameter space sweep, which can then be performed on an arbitrary number of cores with [MultiPlanet](https://github.com/VirtualPlanetaryLaboratory/multi-planet). For large parameter sweeps, an enormous amount of data can be generated, which can slow analyses. To overcome this barrier, the [BigPlanet](https://github.com/VirtualPlanetaryLaboratory/bigplanet) code can both compress datasets into HDF5 format, including statistics of an integration, and tools to facilitate plotting. These three scripts can be executed from the command line to seamlessly [perform parameter sweeps](https://virtualplanetarylaboratory.github.io/vplanet/parametersweep.html). These Python scripts are optimized for [anaconda](https://www.anaconda.com/) distributions versions 3.7-3.9. The "wheels" badge indicates if you can download and install the executables with pip for these Python distributions on the latest Linux and Mac operating systems.
 
 ### Code Integrity
 
-Behind the scenes, the VPLanet team maintains code integrity through via various automatic checks at every merge into the main branch. You can see the status of these checks via the "badges" the GitHub logo above. Currently we perform 5 checks: documentation ("docs"), units tests ("tests"), memory checks via [valgrind](http://valgrind.org) ("memcheck"), confirmation that all [examples](examples/) are working ("examples"), and that the code is pip-installable on Linux, Mac, and Windows machines ("pip-install") for the Python distributions listed. The "coverage" badge shows the percentage of the code (by line number) that is currently tested by <a href="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet">Codecov</a> at every commit. We are committed to maintaining a stable tool for scientists to analyze any planetary system.  
+Behind the scenes, the VPLanet team maintains code integrity through via various automatic checks at every merge into the main branch. You can see the status of these checks via the "badges" the GitHub logo above. Currently we perform 5 checks: documentation ("docs"), units tests ("tests"), memory checks via [valgrind](http://valgrind.org) ("memcheck"), confirmation that all [examples](examples/) are working ("examples"), and that the code is pip-installable on the latest Linux and Mac operating systems ("pip-install") for the Python distributions listed after the GitHub Actions badge. The percentage of the lines of code that are executed by the unit tests is shown with the "codecov" badge, with details available at our <a href="https://codecov.io/gh/VirtualPlanetaryLaboratory/vplanet">Codecov</a> account. We are committed to maintaining a stable tool for scientists to analyze any planetary system.
 
 ### Community
 

diff --git a/src/flare.c b/src/flare.c
@@ -97,49 +97,6 @@ void ReadFlareFFD(BODY *body,
   } else if (iFile > 0)
     body[iFile - 1].iFlareFFD = FLARE_FFD_DAVENPORT;
 }
-/*
-void ReadFlareSlopeUnits(BODY *body,
-                         CONTROL *control,
-                         FILES *files,
-                         OPTIONS *options,
-                         SYSTEM *system,
-                         int iFile) {
-  /* This parameter cannot exist in primary file */
-/*int lTmp = -1;
-char cTmp[OPTLEN];
-
-AddOptionString(files->Infile[iFile].cIn,
-                options->cName,
-                cTmp,
-                &lTmp,
-                control->Io.iVerbose);
-if (lTmp >= 0) {
-  NotPrimaryInput(iFile,
-                  options->cName,
-                  files->Infile[iFile].cIn,
-                  lTmp,
-                  control->Io.iVerbose);
-  if (!memcmp(sLower(cTmp), "se", 2)) {
-    body[iFile - 1].iFlareSlopeUnits = FLARE_SLOPE_SEC;
-  } else if (!memcmp(sLower(cTmp), "mi", 2)) {
-    body[iFile - 1].iFlareSlopeUnits = FLARE_SLOPE_MINUTE;
-  } else if (!memcmp(sLower(cTmp), "ho", 2)) {
-    body[iFile - 1].iFlareSlopeUnits = FLARE_SLOPE_HOUR;
-  } else if (!memcmp(sLower(cTmp), "da", 2)) {
-    body[iFile - 1].iFlareSlopeUnits = FLARE_SLOPE_DAY;
-  } else {
-    if (control->Io.iVerbose >= VERBERR)
-      fprintf(stderr,
-              "ERROR: Unknown argument to %s: %s. Options are SEC, MIN, HOUR "
-              "or DAY.\n",
-              options->cName,
-              cTmp);
-    LineExit(files->Infile[iFile].cIn, lTmp);
-  }
-  UpdateFoundOption(&files->Infile[iFile], options, lTmp, iFile);
-} else if (iFile > 0)
-  body[iFile - 1].iFlareSlopeUnits = FLARE_SLOPE_DAY;
-}*/
 
 void ReadFlareBandPass(BODY *body,
                        CONTROL *control,
@@ -1018,8 +975,8 @@ void FinalizeUpdateLXUVFlare(BODY *body, UPDATE *update, int *iEqn, int iVar,
 // not need this.
 /*void FinalizeUpdateFlareFreqMax(BODY *body, UPDATE *update, int *iEqn, int
   iVar, int iBody, int iFoo) {
-  /* No primary variables for FLARE yet*/
-/*  update[iBody].iaModule[iVar][*iEqn] = FLARE;
+  // No primary variables for FLARE yet
+  //  update[iBody].iaModule[iVar][*iEqn] = FLARE;
   update[iBody].iNumFlareFreqMax              = (*iEqn)++;
 }
 */

diff --git a/src/options.c b/src/options.c
@@ -436,18 +436,14 @@ int iGetNumLines(char cFile[]) {
   FILE *fp;
   char cLine[LINE];
 
-  fprintf(stderr,"File: %s\n",cFile);
-
   fp = fopen(cFile, "r");
   if (fp == NULL) {
     fprintf(stderr, "Unable to open %s.\n", cFile);
     exit(EXIT_INPUT);
   }
 
   memset(cLine, '\0', LINE);
-  // fprintf(stderr,"File: %s\n",cFile);
   while (fgets(cLine, LINE, fp) != NULL) {
-    // fprintf(stderr,"iLine: %d, %s",iNumLines,cLine);
     iNumLines++;
 
     /* Check to see if line is too long. The maximum length of a line is set
@@ -489,8 +485,6 @@ void InitializeInput(INFILE *input) {
   FILE *fp;
   char cLine[LINE];
 
-fprintf(stderr,"File: %s\n",input->cIn);
-
   fp = fopen(input->cIn, "r");
   if (fp == NULL) {
     fprintf(stderr, "Unable to open %s.\n", input->cIn);
@@ -503,23 +497,12 @@ fprintf(stderr,"File: %s\n",input->cIn);
   input->cReactions[0] = 0;
   */
 
-  // fprintf(stderr,"File: %s\n",input->cIn);
   for (iLine = 0; iLine < input->iNumLines; iLine++) {
-    /* Initialize bLineOK */
     input->bLineOK[iLine] = 0;
-
-    /* Now find those lines that are comments or blank
-    for (iPos = 0; iPos < LINE; iPos++) {
-      cLine[iPos] = '\0';
-    }
-    */
     memset(cLine, '\0', LINE);
 
     fgets(cLine, LINE, fp);
-    // fprintf(stderr,"iLine: %d, %s",iLine,cLine);
-    /* Check for # sign or blank line */
     if (CheckComment(cLine, LINE)) {
-      /* Line is OK */
       input->bLineOK[iLine] = 1;
     } else {
       // Is it a blank line?

diff --git a/src/output.c b/src/output.c
@@ -2166,8 +2166,11 @@ void WriteLog(BODY *body, CONTROL *control, FILES *files, MODULE *module,
   double dDt, dTotTime;
 
   /* Get derivatives */
+  fprintf(stderr,"In WriteLog.\n");
   PropertiesAuxiliary(body, control, system, update);
+  fprintf(stderr,"After PropsAux.\n");
   dDt = fdGetTimeStep(body, control, system, update, fnUpdate);
+  fprintf(stderr,"After GetTimeStep.\n");
 
   if (iEnd == 0) {
     sprintf(cTime, "Input");

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -20,7 +20,7 @@
 def vplanet_output(request):
     path = os.path.abspath(os.path.dirname(request.fspath))
     infile = os.path.join(path, "vpl.in")
-    output = vplanet.run(infile, quiet=True, clobber=True, C=True)
+    output = vplanet.run(infile, quiet=False, clobber=True, C=True)
     yield output
     if CLEAN_OUTPUTS:
         for file in (