Finish fluctmatch-3.3.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.3.0
+current_version = 3.3.1
 commit = True
 tag = True
 

CHANGELOG.rst

@@ -2,6 +2,20 @@
 Changelog
 =========
 
+3.3.1 (2018-05-15)
+------------------
+
+* Fixes bug in writing average coordinate file
+* Added log file command-line option
+
+3.3.0 (2018-05-15)
+------------------
+
+* Uses MDAnalysis 0.18.0
+* Fix Merge bug
+* Added logging features
+* Formatted according to PEP8
+
 3.1.0 (2017-11-07)
 ------------------
 

README.rst

@@ -44,9 +44,9 @@ Overview
     :alt: PyPI Package latest release
     :target: https://pypi.python.org/pypi/fluctmatch
 
-.. |commits-since| image:: https://img.shields.io/github/commits-since/tclick/python-fluctmatch/v3.3.0.svg
+.. |commits-since| image:: https://img.shields.io/github/commits-since/tclick/python-fluctmatch/v3.3.1.svg
     :alt: Commits since latest release
-    :target: https://github.com/tclick/python-fluctmatch/compare/v3.3.0...master
+    :target: https://github.com/tclick/python-fluctmatch/compare/v3.3.1...master
 
 .. |wheel| image:: https://img.shields.io/pypi/wheel/fluctmatch.svg
     :alt: PyPI Wheel

docs/conf.py

@@ -26,7 +26,7 @@
 year = u'2014-2017'
 author = u'Timothy Click'
 copyright = '{0}, {1}'.format(year, author)
-version = release = u'3.3.0'
+version = release = u'3.3.1'
 
 pygments_style = 'trac'
 templates_path = ['.']

setup.py

@@ -45,7 +45,7 @@ def read(*names, **kwargs):
 
 setup(
     name="fluctmatch",
-    version="3.3.0",
+    version="3.3.1",
     license="BSD license",
     description="Elastic network model using fluctuation matching.",
     long_description="%s\n%s" % (

src/fluctmatch/__init__.py

@@ -24,7 +24,7 @@
 
 import logging
 
-__version__ = "3.3.0"
+__version__ = "3.3.1"
 
 _MODELS = dict()
 _DESCRIBE = dict()

src/fluctmatch/commands/cmd_convert.py

@@ -53,6 +53,15 @@
     type=click.Path(exists=False, file_okay=True, resolve_path=True),
     help="Trajectory file (e.g. xtc trr dcd)",
 )
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "convert.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-o",
     "--outdir",
@@ -155,14 +164,14 @@
     help="Convert the trajectory file",
 )
 @click.option(
-    "-l",
     "--list",
     "model_list",
     is_flag=True,
     help="List available models with their descriptions")
 def cli(
         topology,
         trajectory,
+        logfile,
         outdir,
         prefix,
         rmin,
@@ -202,7 +211,7 @@ def cli(
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "convert.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_diff.py

@@ -32,6 +32,15 @@
 
 
 @click.command("diff", short_help="Calculate differences between two tables.")
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "diff.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-o",
     "--outdir",
@@ -71,7 +80,7 @@
         resolve_path=True,
     ),
 )
-def cli(outdir, ressep, table1, table2):
+def cli(logfile, outdir, ressep, table1, table2):
     logging.config.dictConfig({
         "version": 1,
         "disable_existing_loggers": False,  # this fixes the problem
@@ -95,7 +104,7 @@ def cli(outdir, ressep, table1, table2):
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "diff.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_entropy.py

@@ -34,6 +34,15 @@
 
 @click.command(
     "entropy", short_help="Calculate the Shannon entropy of residues.")
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "entropy.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-o",
     "--outdir",
@@ -64,7 +73,7 @@
         resolve_path=True,
     ),
 )
-def cli(outdir, ressep, table):
+def cli(logfile, outdir, ressep, table):
     # Setup logger
     logging.config.dictConfig({
         "version": 1,
@@ -89,7 +98,7 @@ def cli(outdir, ressep, table):
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "entropy.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_framediff.py

@@ -35,6 +35,15 @@
 @click.command(
     "framediff",
     short_help="Calculate differences between consecutive frames.")
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "framediff.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-o",
     "--outdir",
@@ -65,7 +74,7 @@
         resolve_path=True,
     ),
 )
-def cli(outdir, ressep, table):
+def cli(logfile, outdir, ressep, table):
     # Setup logger
     logging.config.dictConfig({
         "version": 1,
@@ -90,7 +99,7 @@ def cli(outdir, ressep, table):
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "framediff.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_normdiff.py

@@ -37,6 +37,15 @@
 
 @click.command(
     "normdiff", short_help="Normalize the differences between t and t - dt/2.")
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "normdiff.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-o",
     "--outdir",
@@ -76,7 +85,7 @@
         resolve_path=True,
     ),
 )
-def cli(outdir, ressep, kb, b0):
+def cli(logfile, outdir, ressep, kb, b0):
     # Setup logger
     logging.config.dictConfig({
         "version": 1,
@@ -101,7 +110,7 @@ def cli(outdir, ressep, kb, b0):
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "normdiff.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_run_fm.py

@@ -50,6 +50,15 @@
     type=click.Path(exists=False, file_okay=True, resolve_path=True),
     help="Trajectory file (e.g. xtc trr dcd)",
 )
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "charmmfm.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-o",
     "outdir",
@@ -142,6 +151,7 @@
 def cli(
         topology,
         trajectory,
+        logfile,
         outdir,
         nma_exec,
         temperature,
@@ -177,7 +187,7 @@ def cli(
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "charmmfm.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_sca.py

@@ -26,6 +26,7 @@
 
 import logging
 import logging.config
+import os
 from os import path
 
 import click
@@ -39,6 +40,15 @@
 @click.command(
     "sca",
     short_help="Statistical coupling analysis (SCA) on coupling strength")
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "fluctsca.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-n",
     "--ntrials",
@@ -123,7 +133,7 @@
         file_okay=True,
         resolve_path=True,
     ))
-def cli(ntrials, std, kpos, pcut, ressep, output, subset, transformation,
+def cli(logfile, ntrials, std, kpos, pcut, ressep, output, subset, transformation,
         filename):
     # Setup logger
     logging.config.dictConfig({
@@ -149,7 +159,7 @@ def cli(ntrials, std, kpos, pcut, ressep, output, subset, transformation,
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(path.dirname(filename), "fluctsca.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_splittraj.py

@@ -109,15 +109,11 @@
 )
 @click.option(
     "-l",
-    "logfile",
-    metavar="FILE",
-    default="split.log",
+    "--logfile",
+    metavar="LOG",
     show_default=True,
-    type=click.Path(
-        exists=False,
-        file_okay=True,
-        resolve_path=False,
-    ),
+    default=path.join(os.getcwd(), "splittraj.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
     help="Log file",
 )
 @click.option(
@@ -181,7 +177,7 @@ def cli(program, toppar, topology, trajectory, data, index, outfile, logfile,
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(path.dirname(outfile), "splittraj.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",

src/fluctmatch/commands/cmd_stats.py

@@ -34,6 +34,15 @@
 
 
 @click.command("stats", short_help="Calculate statistics of a table.")
+@click.option(
+    "-l",
+    "--logfile",
+    metavar="LOG",
+    show_default=True,
+    default=path.join(os.getcwd(), "convert.log"),
+    type=click.Path(exists=False, file_okay=True, resolve_path=True),
+    help="Log file",
+)
 @click.option(
     "-s",
     "--stats",
@@ -86,7 +95,7 @@
         resolve_path=True,
     ),
 )
-def cli(stats, hist, outdir, ressep, tbltype, table):
+def cli(logfile, stats, hist, outdir, ressep, tbltype, table):
     # Setup logger
     logging.config.dictConfig({
         "version": 1,
@@ -111,7 +120,7 @@ def cli(stats, hist, outdir, ressep, tbltype, table):
             },
             "file": {
                 "class": "logging.FileHandler",
-                "filename": path.join(outdir, "stats.log"),
+                "filename": logfile,
                 "level": "INFO",
                 "mode": "w",
                 "formatter": "detailed",