Add Any type to built-in types (#11)

Add Any type - Add test for Any type - Install `cwltool` with `pipx` to avoid library conflicts. - Remove Ubuntu from test platforms (pypa/pipx#597) Co-authored-by: Bogdan Gavrilovic <[email protected]> Co-authored-by: Kaushik Ghose <[email protected]>
rabix · Jan 14, 2021 · cda5131 · cda5131
1 parent ff611ae
commit cda5131
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Showing 3 changed files with 17 additions and 6 deletions.
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -7,7 +7,10 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        # pipx ensurepath on ubuntu has an issue
+        # https://github.com/pipxproject/pipx/issues/597
+        #os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [macos-latest, windows-latest]
         python-version: [3.6, 3.7, 3.8]
 
     steps:
@@ -19,7 +22,6 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install cwltool
         pip install .
     - name: Lint with flake8
       run: |
@@ -28,11 +30,18 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Install test dependencies
+      run: |
+        pip install pytest
+        pip install pipx
+        pipx install cwltool
+        pipx ensurepath
+    # Need a new shell so that ensurepath takes
     - name: Test with pytest
       env:
         SB_AUTH_TOKEN: ${{ secrets.API_KEY }}
-        SB_API_ENDPOINT: https://api.sbgenomics.com/v2
+        SB_API_ENDPOINT: https://api.sbgenomics.com/v2      
       run: |
-        pip install pytest
+        echo $PATH
         cd tests
-        py.test
+        py.test
diff --git a/sbpack/lib.py b/sbpack/lib.py
@@ -35,7 +35,7 @@ class MissingKeyField(BaseException):
     pass
 
 
-built_in_types = ["null", "boolean", "int", "long", "float", "double", "string",  "File", "Directory", "stdout", "stderr"]
+built_in_types = ["null", "boolean", "int", "long", "float", "double", "string",  "File", "Directory", "stdout", "stderr", "Any"]
 magic_string = "##sbpack_rename_user_type##"
 
 

diff --git a/tests/tools/clt1.cwl b/tests/tools/clt1.cwl
@@ -27,6 +27,8 @@ inputs:
 #     type: ../types/singletype2.yml#simple_record2
   in4:
     type: [string, ../types/recursive.yml#sample_meta]
+  in5:
+    type: Any?
 
 outputs:
   out1:
-Original file line number
+Diff line change
@@ Expand Up / @@ -35,7 +35,7 @@ class MissingKeyField(BaseException): @@
         pass
-    built_in_types = ["null", "boolean", "int", "long", "float", "double", "string",  "File", "Directory", "stdout", "stderr"]
+    built_in_types = ["null", "boolean", "int", "long", "float", "double", "string",  "File", "Directory", "stdout", "stderr", "Any"]
     magic_string = "##sbpack_rename_user_type##"
@@ Expand Down @@