Disable R, Julia, and Seq for testing

Fix model driver test Add gcc standard library
cropsinsilico · May 22, 2024 · 7681680 · 7681680
1 parent 0ecb579
commit 7681680
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Showing 4 changed files with 16 additions and 19 deletions.
diff --git a/.github/workflows/test-install.yml b/.github/workflows/test-install.yml
@@ -7,17 +7,17 @@ env:
   INSTALLEXCEL: 1
   INSTALLFORTRAN: 1
   INSTALLIMAGES: 1
-  INSTALLJULIA: 1
+  INSTALLJULIA: 0
   INSTALLLPY: 0
   INSTALLMATLAB: 0
   INSTALLMPI: 1
   INSTALLOMP: 1
   INSTALLPYGMENTS: 1
   INSTALLPYTORCH: 1
-  INSTALLR: 1
+  INSTALLR: 0
   INSTALLRMQ: 0
   INSTALLSBML: 0
-  INSTALLSEQ: 1
+  INSTALLSEQ: 0
   INSTALLTRIMESH: 1
   INSTALLZMQ: 1
   NUMPY: numpy
@@ -325,8 +325,7 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
-    - if: matrix.install-r != true
-      name: Set R installation based on matrix value
+    - name: Set R installation based on matrix value
       run: echo "INSTALLR=0" >> $GITHUB_ENV
       shell: bash -l {0}
     - if: matrix.install-pytorch != true
@@ -733,8 +732,7 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
-    - if: matrix.install-r != true
-      name: Set R installation based on matrix value
+    - name: Set R installation based on matrix value
       run: echo "INSTALLR=0" >> $GITHUB_ENV
       shell: bash -l {0}
     - if: matrix.install-pytorch != true
@@ -1117,8 +1115,7 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
-    - if: matrix.install-r != true
-      name: Set R installation based on matrix value
+    - name: Set R installation based on matrix value
       run: echo "INSTALLR=0" >> $GITHUB_ENV
       shell: bash -l {0}
     - if: matrix.install-pytorch != true
@@ -1482,8 +1479,7 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
-    - if: matrix.install-r != true
-      name: Set R installation based on matrix value
+    - name: Set R installation based on matrix value
       run: echo "INSTALLR=0" >> $GITHUB_ENV
       shell: bash -l {0}
     - if: matrix.install-pytorch != true
@@ -1846,8 +1842,7 @@ jobs:
       name: Set SBML installation based on matrix value
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
-    - if: matrix.install-r != true
-      name: Set R installation based on matrix value
+    - name: Set R installation based on matrix value
       run: echo "INSTALLR=0" >> $GITHUB_ENV
       shell: bash -l {0}
     - if: matrix.install-pytorch != true

diff --git a/tests/drivers/test_ModelDriver.py b/tests/drivers/test_ModelDriver.py
@@ -7,7 +7,8 @@
 import logging
 from yggdrasil import platform, constants
 from yggdrasil.drivers.ModelDriver import ModelDriver
-from yggdrasil.drivers.CompiledModelDriver import CompiledModelDriver
+from yggdrasil.drivers.CompiledModelDriver import (
+    CompiledModelDriver, InvalidCompilationTool)
 from yggdrasil.drivers.InterpretedModelDriver import InterpretedModelDriver
 
 
@@ -19,7 +20,7 @@ def test_ModelDriver_implementation():
         ModelDriver.executable_command(None)
     with pytest.raises(NotImplementedError):
         ModelDriver.is_library_installed(None)
-    with pytest.raises(NotImplementedError):
+    with pytest.raises(InvalidCompilationTool):
         CompiledModelDriver.get_tool('compiler')
     with pytest.raises(NotImplementedError):
         InterpretedModelDriver.get_interpreter()

diff --git a/utils/test-install-base.yml b/utils/test-install-base.yml
@@ -12,19 +12,19 @@ name: Test of package installation & execution
 
 env:
   NUMPY: numpy
-  INSTALLR: 1
+  INSTALLR: 0  # TODO: temp
   INSTALLC: 1
   INSTALLFORTRAN: 1
   INSTALLSBML: 0
   INSTALLLPY: 0
-  INSTALLJULIA: 1
+  INSTALLJULIA: 0  # TODO: temp
   INSTALLZMQ: 1
   INSTALLRMQ: 0
   INSTALLTRIMESH: 1
   INSTALLPYGMENTS: 1
   INSTALLPYTORCH: 1
   INSTALLIMAGES: 1
-  INSTALLSEQ: 1
+  INSTALLSEQ: 0  # TODO: temp
   INSTALLEXCEL: 1
   INSTALLOMP: 1
   INSTALLMPI: 1
@@ -107,7 +107,7 @@ jobs:
       run: echo "INSTALLSBML=1" >> $GITHUB_ENV
       shell: bash -l {0}
     - name: Set R installation based on matrix value
-      if: matrix.install-r != true
+      # if: matrix.install-r != true  # TODO: temp
       run: echo "INSTALLR=0" >> $GITHUB_ENV
       shell: bash -l {0}
     - name: Set Pytorch installation based on matrix value

diff --git a/yggdrasil/drivers/CModelDriver.py b/yggdrasil/drivers/CModelDriver.py
@@ -132,6 +132,7 @@ class GCCCompiler(CCompilerBase):
     default_linker = 'gcc'
     default_disassembler = 'objdump'
     toolset = 'gnu'
+    standard_library = 'c'
     compatible_toolsets = ['llvm']
     aliases = ['gnu-cc', 'gnu-gcc']
     libraries = {