nifstd-tools setup.py MANIFEST.in rework to include resources

currently not including the inputs for parcellation, but am including
the inputs for neurondm since those do sort of stand alone from the
ontology in a way that the parcellation inputs currently do not

also include the rpmbuild symlinks, this should make it straight
forward to build rpms for specific release, though clearly the spec
files should be able to change independent of the release, so this is
a convenience when it works

and for a good old lolpython time, still no spaces in manifest files
apparently

neurondm/README.md

@@ -37,19 +37,6 @@ config.write()
 config.write_python()
 ```
 
-### NIF-Ontology
-To work with the NIF-Ontology and build existing models
-you need to clone the ontology repository and set your
-SciGraph API key or set up a local SciGraph instance.
-
-```bash
-git clone https://github.com/SciCrunch/NIF-Ontology.git
-ontutils set ontology-local-repo ./NIF-Ontology
-pushd ./NIF-Ontology
-git checkout neurons
-popd
-```
-
 ### SciGraph API
 Set the API key in a separate terminal to avoid losing
 additional history after setting the api key.
@@ -63,6 +50,19 @@ Once that is done you should be able to run the following.
 python -m neurondm.models.huang2017
 ```
 
+### NIF-Ontology
+To work with the NIF-Ontology and build existing models
+you need to clone the ontology repository and set your
+SciGraph API key or set up a local SciGraph instance.
+
+```bash
+git clone https://github.com/SciCrunch/NIF-Ontology.git
+ontutils set ontology-local-repo ./NIF-Ontology
+pushd ./NIF-Ontology
+git checkout neurons
+popd
+```
+
 ### Further configuration
 If you need more details on configuration see the pyontutils
 [configuration](https://github.com/tgbugs/pyontutils/#configuration) section.

neurondm/setup.py

@@ -27,8 +27,6 @@ def _ontology_data_files():
                 'ttl/phenotype-indicators.ttl',
                 'ttl/phenotypes.ttl',
                 'ttl/generated/part-of-self.ttl',]
-    respaths = ['26451489 table 1.csv',
-                'common-usage-types.csv',]
     if RELEASE:
         from augpathlib import RepoPath as Path
         ### KILL IT WITH FIRE
@@ -56,24 +54,23 @@ def _ontology_data_files():
 
         resources = Path(resources)
         resources.mkdir()  # if we add resources to git, this will error before we delete by accident
-        _resources_path = Path(auth.get_path('resources'))
-        paths = ([olr / rp for rp in relpaths] +
-                 [_resources_path / rp for rp in respaths])
+        paths = [olr / rp for rp in relpaths]
         for p in paths:
             p.copy_to(resources / p.name)
 
     else:
         from pathlib import Path
         resources = Path(resources)
-        paths = [Path(rp) for rp in relpaths + respaths]
+        paths = [Path(rp) for rp in relpaths]
 
     return resources.absolute(), [(resources / p.name).as_posix() for p in paths]
 
 
 resources, ontology_data_files = _ontology_data_files()
 print('ontology_data_files:\n\t' + '\n\t'.join(ontology_data_files))
 
-tests_require = ['pytest']
+models_require = ['nifstd-tools>=0.0.6']
+tests_require = ['pytest'] + models_require
 try:
     setup(
         name='neurondm',
@@ -104,6 +101,7 @@ def _ontology_data_files():
         ],
         extras_require={'dev': ['pytest-cov', 'wheel'],
                         'test': tests_require,
+                        'models': models_require,
                         'notebook': ['jupyter'],
         },
         entry_points={

nifstd/MANIFEST.in

@@ -13,7 +13,19 @@ recursive-exclude scigraph *
 recursive-exclude * *.pyc
 recursive-exclude * *.swp
 recursive-exclude * *.swo
+recursive-exclude * *.rpm
 recursive-include resources *.confd
 recursive-include resources *.rc
+recursive-include resources *.socket
+recursive-include resources *.service
+recursive-include resources *.spec
 recursive-include resources *.el
+recursive-include resources *.yaml
 recursive-include resources/sparc_term_versions *
+include resources/ontree.tmp
+include resources/neuron_phenotype.csv
+include resources/26451489*
+include resources/neuron_phenotype.csv
+include resources/common-usage-types.csv
+include resources/neuron_phenotype_edges.csv
+recursive-exclude resources/rpmbuild/BUILD *

nifstd/resources/nifstd-tools.spec

@@ -0,0 +1,91 @@
+# you must build this with --nodeps if you are not on a RHEL alike
+%define     _unitdir       /lib/systemd/system
+%define     _etcdir        /etc/systemd/system
+
+# building on gentoo makes this /var/lib for some reason :/
+%define     _localstatedir /var
+
+%define     nt_user  nifstd-tools
+%define     nt_group %{nifstd-tools}
+%define     nt_home  %{_localstatedir}/lib/nifstd-tools
+%define     nt_log   %{_localstatedir}/log/nifstd-tools
+
+%define     name nifstd-tools
+%define     version 9999
+Name:       %{name}
+Version:    %{version}
+Release:    0
+Summary:    utilities for working with the NIF ontology
+License:    MIT
+Url:        https://github.com/tgbugs/pyontutils/tree/nifstd
+BuildArch:  noarch
+BuildRequires: systemd
+BuildRequires: git
+Requires:   gcc
+Requires:   bash
+Requires:   nginx
+Requires:   python3
+Requires:   python3-devel
+Requires(post):    systemd
+Requires(preun):   systemd
+Requires(postun):  systemd
+
+Source1: ontree.socket
+Source2: ontree.service
+Source3: ontree.confd
+Source4: ontree.tmp
+
+%description
+curation workflow automation and coordination
+
+%prep
+
+if [[ ! -d %{buildroot} ]]; then
+	mkdir %{buildroot};
+fi
+
+%define gitroot pyontutils
+if [[ ! -d %{gitroot} ]]; then
+	git clone https://github.com/tgbugs/pyontutils.git
+fi
+
+%build
+#pushd %{gitroot}
+#python3 setup.py bdist_wheel
+#%py3_build
+
+%install
+install -p -D -m 644 %{SOURCE1} %{buildroot}/%{_unitdir}/ontree.socket
+install -p -D -m 644 %{SOURCE2} %{buildroot}/%{_unitdir}/ontree.service
+install -p -D -m 600 %{SOURCE3} %{buildroot}/%{_etcdir}/ontree.service.d/env.conf
+install -p -D -m 644 %{SOURCE4} %{buildroot}/etc/tmpfiles.d/ontree.conf
+#%py3_install
+
+%pre
+getent group %{nt_group} > /dev/null || groupadd -r %{nt_group}
+getent passwd %{nt_user} > /dev/null || \
+    useradd -r -m -d %{nt_home} -g %{nt_group} \
+    -s /bin/bash -c "nifstd-tools services" %{nt_user}
+if [[ ! -d %{ontree_log} ]]; then
+	mkdir %{ontree_log}  # owner?
+	chown %{nt_user}:%{nt_group} %{ontree_log}
+fi
+
+%post
+systemd-tmpfiles --create
+systemctl enable ontree
+#systemctl enable nginx
+
+%clean
+rm -rf %{buildroot}
+
+%files
+%{_unitdir}/ontree.socket
+%{_unitdir}/ontree.service
+%{_etcdir}/ontree.service.d/env.conf
+/etc/tmpfiles.d/ontree.conf
+#/etc/nginx/nginx.conf
+#/etc/nginx/scibot.conf
+
+%changelog
+# skip this for now

nifstd/resources/rpmbuild/SOURCES/ontree.confd

@@ -0,0 +1 @@
+../../ontree.confd

nifstd/resources/rpmbuild/SOURCES/ontree.service

@@ -0,0 +1 @@
+../../ontree.service

nifstd/resources/rpmbuild/SOURCES/ontree.socket

@@ -0,0 +1 @@
+../../ontree.socket

nifstd/resources/rpmbuild/SOURCES/ontree.tmp

@@ -0,0 +1 @@
+../../ontree.tmp

nifstd/resources/rpmbuild/SPECS/nifstd-tools.spec

@@ -0,0 +1 @@
+../../nifstd-tools.spec

nifstd/setup.py

@@ -1,4 +1,5 @@
 import re
+from pathlib import Path
 from setuptools import setup
 
 
@@ -46,7 +47,7 @@ def find_version(filename):
         'networkx',
         'psutil',
         'pymysql',
-        'pyontutils>=0.1.25',
+        'pyontutils>=0.1.26',
         'sqlalchemy',
     ],
     extras_require={'dev': ['mysql-connector',
@@ -67,5 +68,8 @@ def find_version(filename):
         ],
     },
     data_files=[('share/nifstd/resources/sparc_term_versions/',
-                 ['resources/sparc_term_versions/sparc_terms2-mod.txt'])]
-)
+                 ['resources/sparc_term_versions/sparc_terms2-mod.txt']),
+                ('share/nifstd/resources/',
+                 [p.as_posix() for p in Path('resources').iterdir()
+                  if p.is_file() and p.suffix[1:] not in
+                  ('confd', 'rc', 'service', 'socket', 'tmp', 'spec')],)])