Merge branch 'release/2.2.3'

CHANGES.md

@@ -1,6 +1,10 @@
 
 ## Release Notes
 
+**v2.2.3 - April 3, 2023** 
+
+* **FIXED**: GAIA DR2 stars not getting matched as synonyms in default algorithm.  
+
 **v2.2.2 - May 18, 2022** 
 
 **FIXED**: NED name parsing errors fixed

CITATION.cff

@@ -0,0 +1,12 @@
+cff-version: 1.2.0
+title: sherlock
+message: If you use this software, please cite it as below.
+authors:
+- family-names: "Young"
+  given-names: "David R."
+  orcid: "https://orcid.org/0000-0002-1229-2499"
+doi: 10.5281/zenodo.7970743
+url: "https://github.com/thespacedoctor/sherlock"
+abstract: mine a library of historical and on-going astronomical survey data in an attempt to identify the sources of transient/variable events, and predict their classifications based on crossmatched data.
+keywords: [astronomy]
+license: GPL-3.0-only

MANIFEST.in

@@ -12,3 +12,6 @@ recursive-exclude */tests *
 recursive-exclude */*/tests *
 recursive-exclude */*/*/tests *
 recursive-exclude tests
+prune tests*
+global-exclude *_test.py
+global-exclude tests

README.md

@@ -1,5 +1,9 @@
 # sherlock
 
+
+[![](https://zenodo.org/badge/42115533.svg)](https://zenodo.org/badge/latestdoi/42115533) 
+
+
 <!-- INFO BADGES -->  
 
 [![](https://img.shields.io/pypi/pyversions/qub-sherlock)](https://pypi.org/project/qub-sherlock/)  
@@ -23,3 +27,20 @@ Documentation for sherlock is hosted by [Read the Docs](https://qub-sherlock.rea
 ## Features
 
 * 
+
+
+
+## How to cite sherlock
+
+If you use `sherlock` in your work, please cite using the following BibTeX entry: 
+
+```bibtex
+@software{Young_sherlock,
+    author = {Young, David R.},
+    doi = {10.5281/zenodo.8038058},
+    license = {GPL-3.0-only},
+    title = {{sherlock}},
+    url = {https://github.com/thespacedoctor/sherlock}
+}
+```
+

docs/requirements.txt

@@ -12,3 +12,6 @@ git+https://github.com/readthedocs/readthedocs-sphinx-search@main
 docopt
 unicodecsv
 psutil>5.7
+jinja2==3.0.0
+Markdown==3.3.4
+importlib-metadata==4.13.0

docs/source/conf.py

@@ -12,14 +12,16 @@
 import codecs
 
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.todo',
-              'sphinx.ext.mathjax', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.linkcode', 'sphinxcontrib.mermaid', 'sphinx_search.extension']
+              'sphinx.ext.mathjax', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.linkcode', 'sphinxcontrib.mermaid', 'sphinx_search.extension', 'sphinx.ext.imgconverter']
 
 
 class Mock(MagicMock):
     """AVOID INSTALLING THESE C-DEPENDENT PACKAGES"""
     @classmethod
     def __getattr__(cls, name):
         return Mock()
+
+
 MOCK_MODULES = ['numpy', 'scipy', 'matplotlib', 'matplotlib.colors',
                 'matplotlib.pyplot', 'matplotlib.cm', 'matplotlib.path', 'matplotlib.patches', 'matplotlib.projections', 'matplotlib.projections.geo', 'healpy', 'astropy', 'astropy.io', 'pylibmc', 'ligo', 'ligo.gracedb', 'ligo.gracedb.rest', 'pandas', 'HMpTy', 'HMpTy.mysql', 'HMpTy.htm']
 sys.modules.update((mod_name, Mock()) for mod_name in MOCK_MODULES)
@@ -56,7 +58,7 @@ def __getattr__(cls, name):
     # Toc options
     'collapse_navigation': True,
     'sticky_navigation': True,
-    'navigation_depth': 4,
+    'navigation_depth': 1,
     'includehidden': True,
     'titles_only': False,
     'github_user': 'thespacedoctor',
@@ -263,7 +265,7 @@ def generateAutosummaryIndex():
     # FOR SUBPACKAGES USE THE SUBPACKAGE TEMPLATE INSTEAD OF DEFAULT MODULE
     # TEMPLATE
     if len(allModules):
-        thisText  = """
+        thisText = """
 Modules
 -------
 
@@ -437,6 +439,7 @@ def setup(app):
                          markdown_parser_config, True)
     app.add_transform(AutoStructify)
 
+
 # DO THE WORK
 updateUsageMd()
 autosummaryText = generateAutosummaryIndex()

makefile

@@ -0,0 +1,7 @@
+fulltest:
+	pytest -v -s --profile-svg --profile
+	for i in prof/*.prof; do gprof2dot -f pstats $i | dot -Tsvg -o $i.svg; done
+
+litetest:
+	pytest  -m "not full" -v -s --profile-svg --profile
+	for i in prof/*.prof; do gprof2dot -f pstats $i | dot -Tsvg -o $i.svg; done

pytest.ini

@@ -0,0 +1,5 @@
+[pytest]
+markers =
+    slow: marks tests as slow (deselect with '-m "not slow"')
+    full: mark test to run only in full test (deselect with '-m "not full"')
+    serial

setup.py

@@ -9,6 +9,7 @@ def readme():
     with open(moduleDirectory + '/README.md') as f:
         return f.read()
 
+
 install_requires = [
     'pyyaml',
     'qub-sherlock',
@@ -51,7 +52,7 @@ def readme():
       author='David Young',
       author_email='davidrobertyoung@gmail.com',
       license='MIT',
-      packages=find_packages(),
+      packages=find_packages(exclude=["*tests*"]),
       include_package_data=True,
       install_requires=install_requires,
       test_suite='nose2.collector.collector',

sherlock/__version__.py

@@ -1 +1 @@
-__version__ = '2.2.2'
+__version__ = '2.2.3'

sherlock/advanced_settings.yaml

@@ -9,7 +9,7 @@ version: 1
 database-batch-size: 20000
 cpu-pool-size: False
 
-stop-search-on-synonym-match: False
+stop-search-on-synonym-match: True
 
 ## SEARCH ALGORITHM SETTINGS
 ned stream search radius arcec: 900
@@ -109,6 +109,7 @@ search algorithm:
             association: BS
         general:
             angular radius arcsec: 2.5
+            synonym: VS
             association: VS
     gaia galaxy:
         database table: tcs_view_unclear_gaia_dr2

sherlock/resources/package.mplstyle

@@ -0,0 +1,114 @@
+
+
+
+ps.papersize      : A4   # auto, letter, legal, ledger, A0-A10, B0-B10
+
+### LINES
+lines.linewidth   : 1.0     # line width in points
+lines.linestyle   : -       # solid line
+lines.color       : blue    # has no affect on plot(); see axes.color_cycle
+lines.marker      : None    # the default marker
+lines.markeredgewidth  : 0.3     # the line width around the marker symbol
+lines.markersize  : 8            # markersize, in points
+lines.antialiased : True         # render lines in antialised (no jaggies)
+
+### FONT
+# When text.usetex is False, font.family may also be one or more concrete font names.
+font.family         : sans-serif # serif, sans-serif, cursive, fantasy, monospace
+font.style          : normal # normal, italic, oblique
+font.variant        : normal # normal, small-caps
+font.weight         : medium # normal, bold, bolder, lighter, 100, 200, 300, ..., 900
+font.stretch        : normal # ultra-condensed, extra-condensed, condensed, semi-condensed, normal, semi-expanded, expanded, extra-expanded, ultra-expanded, wider, narrower
+font.size           : 12.0
+
+
+### AXES
+#axes.hold           : True    # whether to clear the axes by default on
+axes.facecolor      : white   # axes background color
+axes.edgecolor      : 002b36    # axes edge color
+axes.linewidth      : 2.0     # edge linewidth
+axes.grid           : True   # display grid or not
+axes.titlesize      : large   # xx-small, x-small, small, medium, large, x-large, xx-large, larger, smaller
+axes.labelsize      : medium  # xx-small, x-small, small, medium, large, x-large, xx-large, larger, smaller
+axes.labelweight    : normal  # normal, bold, bolder, lighter, 100, 200, 300, ..., 900
+axes.labelcolor     : 002b36
+axes.axisbelow      : False   # gridlines and ticks are below the axes elements
+axes.formatter.limits : -5, 5 # use scientific notation if log10 of the axis range is smaller than the first or larger than the second
+axes.formatter.use_locale : False
+axes.formatter.use_mathtext : False
+axes.unicode_minus  : True    # use unicode for the minus symbol rather than hyphen.  See
+axes.prop_cycle : cycler('color', ["dc322f", "268bd2", "859900", "2aa198", "d33682", "cb4b16", "6c71c4", "b58900"])  # color cycle for plot lines (blue, red, green, cyan, magneta, orange, violet, yellow)
+
+### TICKS
+xtick.major.size     : 6     # major tick size in points
+xtick.minor.size     : 3      # minor tick size in points
+xtick.major.width    : 0.9    # major tick width in points
+xtick.minor.width    : 0.9    # minor tick width in points
+xtick.major.pad      : 4      # distance to major tick label in points
+xtick.minor.pad      : 2      # distance to the minor tick label in points
+xtick.color          : 002b36      # color of the tick labels
+xtick.labelsize      : small # xx-small, x-small, small, medium, large, x-large, xx-large, larger, smaller
+xtick.direction      : in     # direction: in, out, or inout
+ytick.major.size     : 6     # major tick size in points
+ytick.minor.size     : 3      # minor tick size in points
+ytick.major.width    : 0.9    # major tick width in points
+ytick.minor.width    : 0.9    # minor tick width in points
+ytick.major.pad      : 4      # distance to major tick label in points
+ytick.minor.pad      : 2      # distance to the minor tick label in points
+ytick.color          : 002b36      # color of the tick labels
+ytick.labelsize      : small # xx-small, x-small, small, medium, large, x-large, xx-large, larger, smaller
+ytick.direction      : in     # direction: in, out, or inout
+
+
+### GRIDS
+grid.color       :   002b36   # grid color
+grid.linestyle   :   :       # dotted
+grid.linewidth   :   0.5     # in points
+grid.alpha       :   0.7     # transparency, between 0.0 and 1.0
+
+
+### LEGEND
+legend.fancybox      : False  # if True, use a rounded box for the legend, else a rectangle
+legend.numpoints     : 1      # the number of points in the legend line
+legend.fontsize      : small
+legend.borderpad     : 0.8    # border whitespace in fontsize units
+legend.markerscale   : 0.8    # the relative size of legend markers vs. original the following dimensions are in axes coords
+legend.labelspacing  : 0.7    # the vertical space between the legend entries in fraction of fontsize
+legend.handlelength  : 1.5    # the length of the legend lines in fraction of fontsize
+legend.handleheight  : 1.0     # the height of the legend handle in fraction of fontsize
+legend.handletextpad : 0.2    # the space between the legend line and legend text in fraction of fontsize
+legend.borderaxespad : 1.0   # the border between the axes and legend edge in fraction of fontsize
+legend.columnspacing : 0.    # the border between the axes and legend edge in fraction of fontsize
+legend.shadow        : False
+legend.frameon       : True   # whether or not to draw a frame around legend
+legend.scatterpoints : 2 # number of scatter points
+
+
+### FIGURE
+figure.figsize   : 8, 6    # figure size in inches
+figure.dpi       : 150      # figure dots per inch
+figure.facecolor : E6E5E5    # figure facecolor; 0.75 is scalar gray
+figure.edgecolor : white   # figure edgecolor
+
+## subplot parameters - dimensions are a fraction of the figure
+figure.subplot.left    : 0.125  # the left side of the subplots of the figure
+figure.subplot.right   : 0.9    # the right side of the subplots of the figure
+figure.subplot.bottom  : 0.1    # the bottom of the subplots of the figure
+figure.subplot.top     : 0.9    # the top of the subplots of the figure
+figure.subplot.wspace  : 0.2    # the amount of width reserved for blank space between subplots
+figure.subplot.hspace  : 0.2    # the amount of height reserved for white space between subplots
+
+
+### SAVING FIGURES
+path.simplify : True   # remove "invisible" points to reduce file size
+path.simplify_threshold : 0.1  # The threshold of similarity below which vertices will be removed
+path.snap : True # When True, rectilinear axis-aligned paths will be snapped to the nearest pixel
+savefig.dpi         : 100      # figure dots per inch
+savefig.facecolor   : white    # figure facecolor when saving
+savefig.edgecolor   : white    # figure edgecolor when saving
+savefig.format      : png      # png, ps, pdf, svg
+savefig.bbox        : standard # 'tight' or 'standard'.
+savefig.pad_inches  : 0.1      # Padding to be used when bbox is set to 'tight'
+
+
+

sherlock/transient_classifier.py

@@ -1263,12 +1263,19 @@ def _print_results_to_stdout(
 
                 printCrossmatches.append(ordDict)
 
+            outputFormat = None
+            # outputFormat = "csv"
+
             from fundamentals.renderer import list_of_dictionaries
             dataSet = list_of_dictionaries(
                 log=self.log,
                 listOfDictionaries=printCrossmatches
             )
-            tableData = dataSet.table(filepath=None)
+
+            if outputFormat == "csv":
+                tableData = dataSet.csv(filepath=None)
+            else:
+                tableData = dataSet.table(filepath=None)
 
             print(tableData)