Merge pull request #315 from sarthakpati/314_script-verification

docs/faq.md

@@ -8,6 +8,7 @@ This page contains answers to frequently asked questions about GaNDLF.
   - [Table of Contents](#table-of-contents)
     - [Why do I get the error `pkg_resources.DistributionNotFound: The 'GANDLF' distribution was not found`?](#why-do-i-get-the-error-pkg_resourcesdistributionnotfound-the-gandlf-distribution-was-not-found)
     - [Where do I start?](#where-do-i-start)
+    - [Why is GaNDLF not working?](#why-is-gandlf-not-working)
     - [Which parts of a GaNDLF configuration are customizable?](#which-parts-of-a-gandlf-configuration-are-customizable)
     - [Can I run GaNDLF on a high performance computing (HPC) cluster?](#can-i-run-gandlf-on-a-high-performance-computing-hpc-cluster)
     - [How can I track the per-epoch training performance?](#how-can-i-track-the-per-epoch-training-performance)
@@ -25,6 +26,12 @@ The [usage](https://cbica.github.io/GaNDLF/usage) guide is fairly comprehensive
 
 [Back To Top ↑](#table-of-contents)
 
+### Why is GaNDLF not working?
+
+Verify that [the installation](https://cbica.github.io/GaNDLF/setup) has been done correctly by running `python ./gandlf_verifyInstall` after activating the correct virtual environment. If you are still having issues, please feel free to [post a support request](https://github.com/CBICA/GaNDLF/issues/new?assignees=&labels=&template=--questions-help-support.md&title=), and we will do our best to address it ASAP.
+
+[Back To Top ↑](#table-of-contents)
+
 ### Which parts of a GaNDLF configuration are customizable?
 
 Virtually all of it! For more details, please see the [usage](https://cbica.github.io/GaNDLF/usage) guide and our extensive [samples](https://github.com/CBICA/GaNDLF/tree/master/samples). All available options are documented in the [config_all_options.yaml file](https://github.com/CBICA/GaNDLF/blob/master/samples/config_all_options.yaml).

docs/setup.md

@@ -35,5 +35,5 @@ pip install -e .
 # conda install -c conda-forge gandlf -y
 
 ## verify installation
-python -c "import GANDLF as gf;print(gf.__version__)"
+python ./gandlf_verifyInstall
 ```

gandlf_verifyInstall

@@ -0,0 +1,46 @@
+#!usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os, argparse
+from datetime import date
+
+
+# main function
+if __name__ == "__main__":
+    copyrightMessage = (
+        "Contact: software@cbica.upenn.edu\n\n"
+        + "This program is NOT FDA/CE approved and NOT intended for clinical use.\nCopyright (c) "
+        + str(date.today().year)
+        + " University of Pennsylvania. All rights reserved."
+    )
+
+    parser = argparse.ArgumentParser(
+        prog="GANDLF_VerifyInstall",
+        formatter_class=argparse.RawTextHelpFormatter,
+        description="Verify GaNDLF installation.\n\n" + copyrightMessage,
+    )
+
+    try:
+        import GANDLF as gf
+
+        print("GaNDLF installed version:", gf.__version__)
+    except:
+        raise Exception(
+            "GaNDLF not properly installed, please see https://cbica.github.io/GaNDLF/setup"
+        )
+
+    try:
+        import GANDLF.anonymize.dicomanonymizer as anon
+
+        if anon:
+            print("GANDLF's git submodules were successfully imported.")
+    except:
+        try:
+            os.system("git submodule update --init --recursive")
+        except:
+            print("Git was not found, please try again.")
+        os.system("pip install -e .")
+
+    args = parser.parse_args()
+
+    print("GaNDLF is ready. See https://cbica.github.io/GaNDLF/usage")

setup.py

@@ -99,6 +99,7 @@ def run(self):
         "gandlf_patchMiner",
         "gandlf_preprocess",
         "gandlf_anonymizer",
+        "gandlf_verifyInstall",
     ],
     classifiers=[
         "Development Status :: 3 - Alpha",