MAINT: Update versioning for pip, Docker

.dockerignore

@@ -7,3 +7,5 @@ data
 *.md
 *.egg-info/
 .circleci/
+docs/
+examples/

.neurodocker.json

@@ -63,16 +63,6 @@
       "user",
       "root"
     ],
-    [
-      "arg",
-      {
-        "VERSION": ""
-      }
-    ],
-    [
-      "run",
-      "echo \"$VERSION\" > /src/fitlins/fitlins/VERSION"
-    ],
     [
       "run",
       "mkdir /work && chown -R neuro /src /work && chmod a+w /work"
@@ -82,21 +72,21 @@
       "neuro"
     ],
     [
-      "miniconda",
+      "arg",
       {
-        "use_env": "neuro",
-        "pip_opts": "-r",
-        "pip_install": [
-          "/src/fitlins/requirements.txt"
-        ]
+        "VERSION": ""
       }
     ],
+    [
+      "run",
+      "echo \"$VERSION\" > /src/fitlins/VERSION"
+    ],
     [
       "miniconda",
       {
         "use_env": "neuro",
         "pip_install": [
-          "/src/fitlins[all,test]"
+          "/src/fitlins[all]"
         ],
         "activate": true
       }

Dockerfile

@@ -1,5 +1,5 @@
 # Generated by Neurodocker version 0.5.0
-# Timestamp: 2019-05-02 14:00:04 UTC
+# Timestamp: 2019-05-09 20:10:42 UTC
 # 
 # Thank you for using Neurodocker. If you discover any issues
 # or ways to improve this software, please submit an issue or
@@ -86,23 +86,17 @@ COPY [".", "/src/fitlins"]
 
 USER root
 
-ARG VERSION
-
-RUN echo "$VERSION" > /src/fitlins/fitlins/VERSION
-
 RUN mkdir /work && chown -R neuro /src /work && chmod a+w /work
 
 USER neuro
 
-RUN bash -c "source activate neuro \
-    &&   pip install --no-cache-dir -r \
-             '/src/fitlins/requirements.txt'" \
-    && rm -rf ~/.cache/pip/* \
-    && sync
+ARG VERSION
+
+RUN echo "$VERSION" > /src/fitlins/VERSION
 
 RUN bash -c "source activate neuro \
     &&   pip install --no-cache-dir  \
-             '/src/fitlins[all,test]'" \
+             '/src/fitlins[all]'" \
     && rm -rf ~/.cache/pip/* \
     && sync \
     && sed -i '$isource activate neuro' $ND_ENTRYPOINT
@@ -189,16 +183,6 @@ RUN echo '{ \
     \n      "root" \
     \n    ], \
     \n    [ \
-    \n      "arg", \
-    \n      { \
-    \n        "VERSION": "" \
-    \n      } \
-    \n    ], \
-    \n    [ \
-    \n      "run", \
-    \n      "echo \"$VERSION\" > /src/fitlins/fitlins/VERSION" \
-    \n    ], \
-    \n    [ \
     \n      "run", \
     \n      "mkdir /work && chown -R neuro /src /work && chmod a+w /work" \
     \n    ], \
@@ -207,21 +191,21 @@ RUN echo '{ \
     \n      "neuro" \
     \n    ], \
     \n    [ \
-    \n      "miniconda", \
+    \n      "arg", \
     \n      { \
-    \n        "use_env": "neuro", \
-    \n        "pip_opts": "-r", \
-    \n        "pip_install": [ \
-    \n          "/src/fitlins/requirements.txt" \
-    \n        ] \
+    \n        "VERSION": "" \
     \n      } \
     \n    ], \
     \n    [ \
+    \n      "run", \
+    \n      "echo \"$VERSION\" > /src/fitlins/VERSION" \
+    \n    ], \
+    \n    [ \
     \n      "miniconda", \
     \n      { \
     \n        "use_env": "neuro", \
     \n        "pip_install": [ \
-    \n          "/src/fitlins[all,test]" \
+    \n          "/src/fitlins[all]" \
     \n        ], \
     \n        "activate": true \
     \n      } \

MANIFEST.in

@@ -1,3 +1,3 @@
 include versioneer.py
-include fitlins/_version.py
-include fitlins/VERSION
+include fitlins/data/*.json
+include fitlins/data/*.tpl

fitlins/_version.py

@@ -15,6 +15,7 @@
 import re
 import subprocess
 import sys
+from pathlib import Path
 
 
 def get_keywords():
@@ -483,10 +484,9 @@ def get_versions():
 
     cfg = get_config()
     verbose = cfg.verbose
-    root_dir = os.path.dirname(__file__)
-    if os.path.isfile(os.path.join(root_dir, 'VERSION')):
-        with open(os.path.join(root_dir, 'VERSION')) as vfile:
-            version = vfile.readline().strip()
+    ver_file = Path(__file__).parent.parent / 'VERSION'
+    if ver_file.is_file():
+        version = ver_file.read_text().splitlines()[0].strip()
 
         return {
             "version": version,

setup.cfg

@@ -36,13 +36,16 @@ install_requires =
 [options.extras_require]
 duecredit = duecredit
 test = coverage
-all = duecredit
 docs =
     sphinx
     sphinxcontrib-apidoc
     sphinx-argparse
     texext
     m2r
+all =
+    %(docs)s
+    %(duecredit)s
+    %(test)s
 
 [options.entry_points]
 console_scripts =
@@ -53,6 +56,10 @@ fitlins =
     data/*.json
     data/*.tpl
 
+[options.exclude_package_data]
+* =
+    examples
+
 [versioneer]
 VCS = git
 style = pep440

setup.py

@@ -6,27 +6,13 @@
 
 def main():
     """ Install entry-point """
-    import os
-    from inspect import getfile, currentframe
-    from fitlins.__about__ import (
-        DOWNLOAD_URL,
-    )
-
-    root_dir = os.path.dirname(os.path.abspath(getfile(currentframe())))
-
-    version = None
-    cmdclass = {}
-    if os.path.isfile(os.path.join(root_dir, 'fitlins', 'VERSION')):
-        with open(os.path.join(root_dir, 'fitlins', 'VERSION')) as vfile:
-            version = vfile.readline().strip()
+    import versioneer
+    from fitlins.__about__ import __version__, DOWNLOAD_URL
 
-    if version is None:
-        import versioneer
-        version = versioneer.get_version()
-        cmdclass = versioneer.get_cmdclass()
+    cmdclass = versioneer.get_cmdclass()
 
     setup(
-        version=version,
+        version=__version__,
         cmdclass=cmdclass,
         download_url=DOWNLOAD_URL,
     )

versioneer.py

@@ -287,6 +287,7 @@
 import re
 import subprocess
 import sys
+from pathlib import Path
 
 
 class VersioneerConfig:
@@ -1404,6 +1405,12 @@ def get_versions(verbose=False):
 
     Returns dict with two keys: 'version' and 'full'.
     """
+    ver_file = Path(__file__).parent / 'VERSION'
+
+    if ver_file.is_file():
+        ver = ver_file.read_text().splitlines()[0].strip()
+        return {"version": ver, 'full': ver}
+
     if "versioneer" in sys.modules:
         # see the discussion in cmdclass.py:get_cmdclass()
         del sys.modules["versioneer"]