version bump for release, more integration test fixes

also change the link to default location of the secrets.yaml
file in the readme to be consistent with other documentation

also run coveralls even on test failure since some modules succeed

in theory the ontology local repo should no longer be needed for test
but have not completely verified that

.travis.yml

@@ -48,3 +48,7 @@ script:
 
 after_success:
   - if [[ $HAS_COVERALLS && $TRAVIS_PYTHON_VERSION == 3.7 ]] ; then coveralls ; fi
+
+after_failure:
+  # for now we want converage even if things fail
+  - if [[ $HAS_COVERALLS && $TRAVIS_PYTHON_VERSION == 3.7 ]] ; then coveralls ; fi

README.md

@@ -17,7 +17,7 @@ from your local copy of this repo.
 1. [~/.config/pyontutils/config.yaml](${HOME}/.config/pyontutils/config.yaml).
 This file can be used to augment the varibles defined in [auth-config.py](./pyontutils/auth-config.py).
 For more details about the config see the [orthauth guide](https://github.com/tgbugs/orthauth/blob/master/docs/guide.org).
-2. [secrets.yaml](${HOME}/.config/pyontutils/secrets.yaml) that you can put wherever
+2. [secrets.yaml](${HOME}/.config/orthauth/secrets.yaml) that you can put wherever
 you want by editing the `auth-stores: secrets: path:` entry in [config.yaml](${HOME}/.config/pyontutils/config.yaml).
 The file mode needs to be set to `0600` so that only you can read and write it.
 It is also advisable to place it inside a folder with a mode set to `0700` since

pyontutils/__init__.py

@@ -1 +1 @@
-__version__ = '0.1.19'
+__version__ = '0.1.20'

pyontutils/make_catalog.py

@@ -1,15 +1,17 @@
 #!/usr/bin/env python3
+from pyontutils.config import auth
 __doc__ = f"""Generate ttl/catalog-*.xml
 
 Usage:
     ont-catalog [options]
     ont-catalog [options] <file> ...
 
 Options:
-    -b --big                    when creating catalog also import big files
-                                reccomend running this option with pypy3
-    -j --jobs=NJOBS             number of parallel jobs to run [default: 9]
-    -d --debug                  break at the end
+    -b --big                        when creating catalog also import big files
+                                    reccomend running this option with pypy3
+    -j --jobs=NJOBS                 number of parallel jobs to run [default: 9]
+    -d --debug                      break at the end
+    -l --ontology-local-repo=OLR    path to ontology [default: {auth.get_path('ontology-local-repo')}]
 
 """
 import os
@@ -19,7 +21,6 @@
 from git import Repo
 from pyontutils.utils import anyMembers
 from pyontutils.core import displayTriples
-from pyontutils.config import auth
 from pyontutils.ontload import local_imports
 try:
     breakpoint
@@ -32,7 +33,7 @@ def main():
     args = docopt(__doc__, version='ont-catalog 0.0.1')
     dobig = args['--big']
     remote_base = 'http://ontology.neuinfo.org/NIF/ttl/'
-    olr = auth.get_path('ontology-local-repo')
+    olr = Path(args['--ontology-local-repo'])
     local_base = (olr / 'ttl').as_posix() + '/'
 
     #list of all nif ontologies

pyontutils/ontutils.py

@@ -323,10 +323,11 @@ def version_iri(filename, epoch):
 
 
 def make_version_iri_from_iri(iri, epoch):
-    pp = PurePath(iri)
+    head, tail = iri.split('/', 1)
+    pp = PurePath(tail)
     vp = (pp.with_suffix('') / 'version' / str(epoch) / pp.stem).with_suffix(pp.suffix)
-    versionIRI = rdflib.URIRef(str(vp))
-    print(versionIRI)
+    viri = head + str(vp)
+    versionIRI = rdflib.URIRef(viri)
     return rdflib.URIRef(versionIRI)
 
 

setup.py

@@ -41,7 +41,7 @@ def find_version(filename):
     tests_require=tests_require,
     install_requires=[
         'appdirs',
-        'augpathlib>=0.0.10',
+        'augpathlib>=0.0.11',
         'colorlog',
         'docopt',
         'gitpython',

test/owl-test.ttl

@@ -0,0 +1,7 @@
+@prefix : <file:///ERROR/EMPTY/PREFIX/BANNED/> .
+@prefix owl: <http://www.w3.org/2002/07/owl#> .
+
+<http://ontology.neuinfo.org/NIF/ttl/nif.ttl> a owl:Ontology ;
+    :asdf <http://example.org/404> .
+
+### Serialized using the ttlser deterministic serializer v1.2.0

test/test_integration.py

@@ -4,6 +4,7 @@
 from pathlib import Path
 from importlib import import_module
 import pytest
+import augpathlib as aug
 import pyontutils
 from pyontutils.utils import get_working_dir
 from pyontutils.config import auth
@@ -30,6 +31,12 @@ def test_query(self):
 class TestScripts(Folders, _TestScriptsBase):
     """ woo ! """
 
+    def setUp(self):
+        super().setUp()
+        _temp_git.init()
+        _test_ttl.copy_outto(_temp_git)
+        _test_owl.copy_outto(_temp_git)
+
 
 TestScripts.temp_path = temp_path
 
@@ -61,32 +68,73 @@ class TestScripts(Folders, _TestScriptsBase):
     import inspect
     sf = inspect.getsourcefile(pyontutils)
     working_dir = Path(sf).parent.parent
-    #working_dir = Path(__file__).parent.parent
+else:
+    class RP(aug.RepoPath):
+        """ can't just change RepoPath._repo_class due to
+            fail in the no commit case """
+        _repo_class = Repo
+
+    RP._bind_flavours()
+    working_dir = RP(working_dir)
 
 glb = auth.get_path('git-local-base')
 olr = auth.get_path('ontology-local-repo')
 if olr.exists():
     ont_repo = Repo(olr)
-    post_load = lambda : (ont_repo.remove_diff_untracked(), ont_repo.checkout_diff_tracked())
-    post_main = lambda : (ont_repo.remove_diff_untracked(), ont_repo.checkout_diff_tracked())
-    do_mains = True
+    if isinstance(working_dir, aug.RepoPath):
+        this_repo = working_dir.repo
+        post_load = lambda : (ont_repo.remove_diff_untracked(),
+                              ont_repo.checkout_diff_tracked(),
+                              this_repo.remove_diff_untracked(),
+                              this_repo.checkout_diff_tracked(),)
+        post_main = lambda : (ont_repo.remove_diff_untracked(),
+                              ont_repo.checkout_diff_tracked(),
+                              this_repo.remove_diff_untracked(),
+                              this_repo.checkout_diff_tracked(),)
+    else:
+        post_load = lambda : (ont_repo.remove_diff_untracked(),
+                              ont_repo.checkout_diff_tracked())
+        post_main = lambda : (ont_repo.remove_diff_untracked(),
+                              ont_repo.checkout_diff_tracked())
 else:
-    post_load = lambda : None
-    post_main = lambda : None
-    do_mains = True
+    if isinstance(working_dir, aug.RepoPath):
+        this_repo = working_dir.repo
+        post_load = lambda : (this_repo.remove_diff_untracked(),
+                              this_repo.checkout_diff_tracked(),)
+        post_main = lambda : (this_repo.remove_diff_untracked(),
+                              this_repo.checkout_diff_tracked(),)
 
-### build mains
+    else:
+        post_load = lambda : None
+        post_main = lambda : None
+
+
+do_mains = True
+
+
+default_dir = aug.AugmentedPath(__file__).parent
+
+_test_ttl = (default_dir / 'graphload-test.ttl')
+test_ttl = _test_ttl.as_posix()
+_test_owl = (default_dir / 'owl-test.ttl')
+test_owl = _test_owl.as_posix()
+_temp_git = aug.RepoPath(temp_path) / 'git-test'
+temp_git = _temp_git.as_posix()
 
-test_ttl = (Path(__file__).parent / 'graphload-test.ttl').as_posix()
-nifttl = (olr / 'ttl/nif.ttl').as_posix()
 nsmethodsobo = (glb / 'methodsOntology/source-material/ns_methods.obo').as_posix()
+
+
+### build mains
+
 mains = {'scigraph':None,
          'combinators':None,
          'hierarchies':None,
          'googapis': None,
          'closed_namespaces':None,
          #'docs':['ont-docs'],  # can't seem to get this to work correctly on travis so leaving it out for now
-         'make_catalog':['ont-catalog', '--jobs', '1'],  # hits the network
+         'make_catalog':['ont-catalog',
+                         '-l', temp_git,
+                         '--jobs', '1'],  # hits the network
          'graphml_to_ttl':['graphml-to-ttl', 'development/methods/methods_isa.graphml'],
 #['ilxcli', '--help'],
          'obo_io':['obo-io', '--ttl', nsmethodsobo],  # this should also fail, but doesn't ?
@@ -99,18 +147,18 @@ class TestScripts(Folders, _TestScriptsBase):
            ],
 'necromancy':['necromancy', '-l', temp_path_ap, '--mkdir', test_ttl],
 'ontload':[['ontload', '--help'],
-           ['ontload', 'chain', 'NIF-Ontology', 'NIF', nifttl,
+           ['ontload', 'chain', 'NIF-Ontology', 'NIF', test_owl,
             '--zip-location', temp_path_ap],  # this hits the network, so why doesn't it fail in sandbox?
            ['ontload', 'config', 'NIF-Ontology', 'NIF',
             '--zip-location', temp_path_ap,],
            ['ontload', 'graph', 'NIF-Ontology', 'NIF',
             '--zip-location', temp_path_ap,
             '--git-local', temp_path_ap,
-            '--graphload-ontologies', (Path(__file__).parent / 'ontologies-test.yaml').resolve().as_posix()],  # FIXME cleanup
+            '--graphload-ontologies', (default_dir / 'ontologies-test.yaml').resolve().as_posix()],  # FIXME cleanup
            ['ontload', 'imports', 'NIF-Ontology', 'NIF', test_ttl]],
 'ontutils':[['ontutils', '--help'],
-            ['ontutils', 'deadlinks', nifttl],
-            ['ontutils', 'version-iri', nifttl],
+            ['ontutils', 'deadlinks', test_owl],
+            ['ontutils', 'version-iri', test_owl],
             #['ontutils', 'spell', test_ttl],  #  FIXME skipping for now due to huspell dependency
             #['ontutils', 'diff', 'test/diff-before.ttl', 'test/diff-after.ttl', 'definition:', 'skos:definition'],
            ],