Merge branch 'development'

Author: sanjayankur31

.mypy.ini

@@ -0,0 +1,2 @@
+[mypy]
+ignore_missing_imports = True

.pre-commit-config.yaml

@@ -0,0 +1,16 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+    - id: trailing-whitespace
+    - id: end-of-file-fixer
+    - id: check-added-large-files
+      args: [ "--maxkb=5000"]
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.4.1
+  hooks:
+    - id: ruff
+      args: [ "--select", "I", "--fix" ]
+    - id: ruff-format

omv/common/inout.py

@@ -1,10 +1,10 @@
-import yaml
-from collections import deque
 import os
-import sys
 
 # import textwrap
 import subprocess as sp
+from collections import deque
+
+import yaml
 
 LINEWIDTH = 70
 __PROMPT__ = "[omv] "
@@ -25,10 +25,7 @@ def omvify(x):
 
 
 def check(b):
-    if sys.version_info >= (3, 0):
-        tick = "\u2714" if b else "\u2718"
-    else:
-        tick = "\u2714" if b else "\u2718"
+    tick = "\u2714" if b else "\u2718"
     return tick
 
 
@@ -57,11 +54,7 @@ def inform(
     else:
         p = pars if pars else ""
         # print("msg is %s"%msg.__class__)
-        msgstr = (
-            msg.encode("utf-8")
-            if sys.version_info[0] == 2 and isinstance(msg, unicode)
-            else str(msg)
-        )
+        msgstr = str(msg)
         infostr = msgstr + str(p)
         block = deque([infostr])
 
@@ -120,29 +113,18 @@ def check_output(cmds, cwd=".", shell=False, verbosity=0, env=None):
         return ret_string
 
     except sp.CalledProcessError as err:
-        inform(
-            "CalledProcessError running commands: %s in %s (return code: %s), output:\n%s"
-            % (cmds, cwd, err.returncode, err.output),
-            indent=2,
-            verbosity=verbosity,
-        )
         inform("Error: %s" % (err), indent=2, verbosity=verbosity)
         raise err
     except Exception as err:
-        inform(
-            "Error running commands: %s in (%s)!" % (cmds, cwd),
-            indent=2,
-            verbosity=verbosity,
-        )
         inform("Error: %s" % (err), indent=2, verbosity=verbosity)
         raise err
 
 
 def pip_install(packages, version=None):
-    pip = "pip3" if sys.version_info.major == 3 else "pip"
+    pip = "pip"
     cmds = [pip, "install"]
-    if type(packages) == str:
-        if version == None:
+    if isinstance(packages, str):
+        if version is None:
             cmds.append(packages)
         else:
             cmds.append("%s==%s" % (packages, version))

omv/engines/getjnml.py

@@ -8,6 +8,7 @@
 
 
 def install_jnml(version):
+    """Install JNeuroML from GitHub tar."""
     if not version:
         version = "v0.14.0"
 

omv/engines/jneuroml.py

@@ -2,41 +2,23 @@
 import shutil
 import subprocess as sp
 from pathlib import Path
-import platform
 
-from omv.common.inout import inform, trim_path, is_verbose, check_output
-from omv.engines.engine import OMVEngine, EngineExecutionError
+from omv.common.inout import check_output, inform, is_verbose, trim_path
+from omv.engines.engine import EngineExecutionError, OMVEngine
 
 
 class JNeuroMLEngine(OMVEngine):
     name = "jNeuroML"
+    e_name = "jnml"
 
     @staticmethod
     def get_environment():
         if "JNML_HOME" in os.environ:
             jnmlhome = os.environ["JNML_HOME"]
-        elif shutil.which("jnml") is not None:
-            jnmlhome = Path(shutil.which("jnml")).parent
+        elif shutil.which(JNeuroMLEngine.e_name) is not None:
+            jnmlhome = Path(shutil.which(JNeuroMLEngine.e_name)).parent
         else:
-            osname = platform.system()
-            if osname == "Linux":
-                try:
-                    jnmlhome = os.path.join(
-                        os.environ["XDG_DATA_HOME"], "jnml/jNeuroMLJar"
-                    )
-                except KeyError:
-                    localsharepath = os.path.join(os.environ["HOME"], ".local/share")
-                    if os.path.isdir(localsharepath):
-                        jnmlhome = os.path.join(
-                            os.environ["HOME"], ".local/share/jnml/jNeuroMLJar"
-                        )
-                    else:
-                        jnmlhome = os.path.join(os.environ["HOME"], "jnml/jNeuroMLJar")
-
-            elif osname == "Darwin":
-                jnmlhome = os.path.join(os.environ["HOME"], "Library/jnml/jNeuroMLJar")
-            else:
-                jnmlhome = os.path.join(os.environ["HOME"], "jnml/jNeuroMLJar")
+            jnmlhome = ""
 
         environment_vars = {"JNML_HOME": jnmlhome}
 
@@ -45,9 +27,7 @@ def get_environment():
     @staticmethod
     def get_executable():
         environment_vars = JNeuroMLEngine.get_environment()
-        jnml = os.path.join(
-            environment_vars["JNML_HOME"], "jnml" if os.name != "nt" else "jnml.bat"
-        )
+        jnml = os.path.join(environment_vars["JNML_HOME"], JNeuroMLEngine.e_name)
         return jnml
 
     @staticmethod
@@ -59,7 +39,6 @@ def is_installed():
                     "Checking whether %s is installed..." % JNeuroMLEngine.name,
                     indent=1,
                 )
-            FNULL = open(os.devnull, "w")
             jnml = JNeuroMLEngine.get_executable()
             r = check_output(
                 [jnml, "-v"], verbosity=2, env=JNeuroMLEngine.get_environment()
@@ -76,10 +55,10 @@ def is_installed():
 
     @staticmethod
     def install(version):
-        from omv.engines.getjnml import install_jnml
+        from omv.engines.getpyneuroml import install_pynml
 
-        inform("Will fetch and install jNeuroML jar", indent=2)
-        install_jnml(version)
+        inform("Will install PyNeuroML for jnml", indent=2)
+        install_pynml(version)
 
         if not JNeuroMLEngine.is_installed():
             inform("Failure to install, exiting", indent=1)

omv/engines/jneuromlvalidate.py

@@ -28,10 +28,14 @@ def run(self):
             path_s = resolve_paths(self.modelpath)
 
             inform(
-                "Path [%s] expanded to: %s" % (self.modelpath, path_s),
+                "Path [%s] expanded to: \n        %s" % (self.modelpath, '\n        '.join(path_s)),
                 indent=1,
                 verbosity=1,
             )
+            if len(path_s) == 0:
+                raise EngineExecutionError(
+                    "Could not determine list of files for validation from string: %s" % self.modelpath
+                )
 
             from omv.engines.jneuroml import JNeuroMLEngine
 

omv/engines/utils/__init__.py

@@ -6,16 +6,22 @@ def resolve_paths(path_s):
     Make explicit list from: '*.nml myfile.xml' etc.
     """
 
-    if "*" in path_s:
-        import glob
+    import glob
+
+    if PATH_DELIMITER in path_s:
+        all_paths = []
+        for p in path_s.split(PATH_DELIMITER):
+            for g in glob.glob(p):
+                print('Found path:', g)
+                all_paths.append(g)
+        path_s = all_paths
+    else:
+        all_paths = []
+
+        for g in glob.glob(path_s):
+            print('Found path:', g)
+            all_paths.append(g)
+        path_s = all_paths
 
-        if PATH_DELIMITER in path_s:
-            all_paths = []
-            for p in path_s.split(PATH_DELIMITER):
-                for g in glob.glob(p):
-                    all_paths.append(g)
-            path_s = all_paths
-        else:
-            path_s = glob.glob(path_s)
 
     return path_s

omv/omv_util.py

@@ -228,9 +228,7 @@ def _install_engine(eng):
             if ee.is_installed():
                 already_installed = True
             else:
-                from omv.engines.getjnml import install_jnml
-
-                install_jnml(engine_version)
+                ee.install(None)
 
         elif eng.lower() == "neuroConstruct" or eng == "Py_neuroConstruct".lower():
             from omv.engines.pyneuroconstruct import PyneuroConstructEngine as ee

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = OSBModelValidation
-version = 0.3.8
+version = 0.3.9
 author = Boris Marin, Padraig Gleeson
 author_email = [email protected]
 url = https://github.com/OpenSourceBrain/osb-model-validation