Merge pull request #16 from rabix/fix/git-ref-local-file

Fix/git ref local file

.github/workflows/tests.yml

@@ -34,7 +34,7 @@ jobs:
  run: |
  pip install pytest
  pip install pipx
- pipx install cwltool
+ pipx install cwltool>=3.0
  pipx ensurepath
  # Need a new shell so that ensurepath takes
  - name: Test with pytest

Readme.md

@@ -175,6 +175,19 @@ You can have several profiles on the same platform if, for example, you
 are an enterprise user and you belong to several divisions. Please refer
 to the API documentation for more detail.
 
+### Reading credentials from env variables
+
+Instead of using the credentials file, you can specify environment variables
+`SB_API_ENDPOINT` and `SB_AUTH_TOKEN`. To use the env variables in `sbpack` simply
+specify profile `.` in the command, e.g.
+
+```bash
+sbpack . kghosesbg/sbpla-31744/ATAC-seq-pipeline-se https://raw.githubusercontent.com/Duke-GCB/GGR-cwl/master/v1.0/ATAC-seq_pipeline/pipeline-se.cwl
+```
+
+By specifying `.` profile, `sbpack` will use env variables. If these are not found, the default profile
+from the credentials file is used.
+
 ### Running the test suite
 
 The pulling test requires two environment variables to be set

requirements.txt

@@ -0,0 +1,3 @@
+ruamel.yaml >= 0.16
+sevenbridges-python >= 2.0
+cwlformat

sbpack/pack.py

@@ -20,14 +20,12 @@
 import enum
 
 from ruamel.yaml import YAML
-
-import sevenbridges as sbg
 import sevenbridges.errors as sbgerr
 
 import sbpack.schemadef as schemadef
 import sbpack.lib as lib
 
-from .version import __version__
+from sbpack.version import __version__
 
 import logging
 

sbpack/version.py

@@ -1 +1 @@
-__version__ = "2020.10.05"
+__version__ = "2021.10.07"

setup.py

@@ -1,6 +1,7 @@
 # Copyright (c) 2020 Seven Bridges. See LICENSE
 
 import pathlib
+import os
 from datetime import datetime
 from setuptools import setup, find_packages
 
@@ -11,18 +12,15 @@
 now = datetime.utcnow()
 desc_path = pathlib.Path(current_path, "Readme.md")
 long_description = desc_path.open("r").read()
+requirements = os.path.join(current_path, 'requirements.txt')
 
 setup(
  name=name,
  version=version,
  packages=find_packages(),
  platforms=['POSIX', 'MacOS', 'Windows'],
  python_requires='>=3.6',
- install_requires=[
- "ruamel.yaml >= 0.16.12",
- "sevenbridges-python >= 0.20.2",
- "cwlformat"
- ],
+ install_requires=open(requirements).read().splitlines(),
  entry_points={
  'console_scripts': [
  'sbpack = sbpack.pack:main',

tests/test_validation_battery.py

@@ -25,12 +25,15 @@ def cwl_is_valid(fname):
  ('f',),
  [("tools/clt1.cwl",), ("tools/clt2.cwl",), ("tools/clt3.cwl",),
  ("workflows/wf1.cwl",), ("workflows/wf2.cwl",), ("workflows/wf4.cwl",),
+ ("workflows/wf-with-git.cwl",),
  ("https://raw.githubusercontent.com/rabix/sbpack/master/tests/workflows/wf1.cwl",),
  ("https://raw.githubusercontent.com/rabix/sbpack/master/tests/workflows/wf2.cwl",),
  ("https://raw.githubusercontent.com/rabix/sbpack/master/tests/workflows/wf4.cwl",),
  ("remote-cwl/tool1.cwl",), ("remote-cwl/tool2.cwl",), ("remote-cwl/wf1.cwl",)
  ]
 )
+@pytest.mark.skipif(sys.platform == 'win32',
+ reason='Skip on windows due to errors in cwltool with import pwd')
 def test_local_packing_with_validation(f):
  url = urllib.parse.urlparse(f)
  packed_name = pathlib.Path(url.path).stem + "-packed.cwl"

tests/workflows/wf-with-git.cwl

@@ -0,0 +1,13 @@
+class: Workflow
+cwlVersion: v1.2
+inputs:
+ in: File
+steps:
+ git:
+ in:
+ - id: file1
+ source: in
+ out:
+ - id: output_file
+ run: https://raw.githubusercontent.com/common-workflow-language/cwl-v1.2/main/tests/cat3-tool-docker.cwl
+