Merge pull request #16 from InformaticsMatters/issue-10

Issue 10

Author: alanbchristie

README.md

@@ -8,8 +8,9 @@ text-file format used to both describe and execute built-in tests.
 ## Execution environment
 You will need: -
 
--   Groovy
 -   Conda
+-   Groovy (v2.4)
+-   Python
 
 Although the project is based on [Gradle], which is Groovy-based,
 you will need to install **Groovy**. We've tested this framework using Groovy
@@ -170,10 +171,46 @@ that can be tested using `setup.py`. To test these modules run the
 following from the `src/python` directory: -
 
     $ python setup.py test
- 
+
+## Considerations for Windows
+The tests and test framework are designed to operate from within a unix-like
+environment but if you are forced to execute pipeline tests from Windows the
+following approach is recommended: -
+
+You will need:
+
+-   Conda
+-   Groovy (v2.4)
+-   Git-Bash
+
+1.  Install [Git for Windows]. This will give you a unix bash-like
+    execution environment
+1.  From within the Git-bash shell navigate to your pipelines project.
+1.  Ensure that you can execute both Python and Groovy from within the
+    Git-Bash shell (i.e. `python --version` and `groovy --version` work)
+1.  From the pipelines project root enter your Conda environment
+    with something like `source activate my-conda-env`. To run the
+    pipelines tests your environment must contain the rdkit package. It
+    can be installed with this command from within Conda...
+    
+    $ conda install -c rdkit rdkit
+    
+1.  Install additional modules required by `pipelines-utils` but
+    using its requirements file (which can be found in the `pipelines-utils`
+    sub-project): -
+    
+    $ pip install -r requirements.txt
+
+With the above steps complete you should be able to execute the pipelines
+tester by navigating to the sub-module in your pipelines project: -
+
+    $ cd pipelines-utils
+    $ ./gradlew runPipelineTester
+
 ---
 
 [Conda]: https://conda.io/docs/
+[Git for Windows]: http://gitforwindows.org
 [Gradle]: https://gradle.org
 [Groovy]: http://groovy-lang.org
 [PIP]: https://pypi.python.org/pypi

requirements.txt

@@ -1,6 +1,5 @@
 # Additional modules we depend on.
 # Required from within an RDKIT Conda environment
 
-matplotlib == 2.1.1
 molvs == 0.0.9
 standardiser == 0.1.9

src/groovy/ContainerExecutor.groovy

@@ -48,7 +48,16 @@ class ContainerExecutor {
         StringBuilder sout = new StringBuilder()
         StringBuilder serr = new StringBuilder()
 
-        // Note: PIN and POUT have trailing forward-slashed for now
+        // Windows/Git-Bash PIN/POUT path tweak...
+        String osName = System.properties['os.name']
+        if (osName && osName.startsWith('Win')) {
+            pin = pin.replace('\\', '/')
+            pin = pin.replace('C:', '/c')
+            pout = pout.replace('\\', '/')
+            pout = pout.replace('C:', '/c')
+        }
+
+        // Note: PIN and POUT have trailing forward-slashes for now
         //       to allow a migratory use of $PIN}file references
         //       rather than insisting on ${PIN}/file which would fail if
         //       PIN wasn't defined - it's about lowest risk changes.

src/groovy/PipelineTester.groovy

@@ -31,7 +31,7 @@
 
 // Version
 // Update with every change/release
-String version = '2.1.0'
+String version = '2.1.1'
 
 println "+----------------+"
 println "| PipelineTester | v$version"

src/groovy/ShellExecutor.groovy

@@ -24,10 +24,12 @@ class ShellExecutor {
 
     /**
      * Executes the given command using the shell in the supplied execution
-     * directory.
+     * directory. Normally this would be executed in a unix-like environment.
+     * In Windows this would be from something like a Git-Bash shell.
      *
      * @param command The command to run
      * @param edir The directory in which to run the command
+     *             (execution directory)
      * @param pin The pipeline input directory
      *            (used to define the PIN environment variable)
      * @param pout The pipeline output directory
@@ -43,6 +45,16 @@ class ShellExecutor {
 
         StringBuilder sout = new StringBuilder()
         StringBuilder serr = new StringBuilder()
+
+        // Windows/Git-Bash PIN/POUT path tweak...
+        String osName = System.properties['os.name']
+        if (osName && osName.startsWith('Win')) {
+            pin = pin.replace('\\', '/')
+            pin = pin.replace('C:', '/c')
+            pout = pout.replace('\\', '/')
+            pout = pout.replace('C:', '/c')
+        }
+
         // Append '/' to PIN and POUT to allow '${POUT}output'
         String cmd = "PIN=$pin/; POUT=$pout/; " + command
         def proc = ['sh', '-c', cmd].execute(null, edir)