Merge pull request #123 from sbillinge/tests

tests

Author: sbillinge

Diff for: .flake8

@@ -0,0 +1,11 @@
+[flake8]
+exclude =
+    .git,
+    __pycache__,
+    build,
+    dist,
+    doc/source/conf.py
+max-line-length = 115
+# Ignore some style 'errors' produced while formatting by 'black'
+# https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#labels-why-pycodestyle-warnings
+extend-ignore = E203

Diff for: .pre-commit-config.yaml

@@ -0,0 +1,43 @@
+default_language_version:
+    python: python3
+ci:
+    autofix_commit_msg: |
+        [pre-commit.ci] auto fixes from pre-commit hooks
+    autofix_prs: true
+    autoupdate_branch: 'pre-commit-autoupdate'
+    autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate'
+    autoupdate_schedule: monthly
+    skip: [no-commit-to-branch]
+    submodules: false
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.6.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        exclude: '\.(rst|txt)$'
+  - repo: https://github.com/psf/black
+    rev: 24.4.2
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8
+  - repo: https://github.com/pycqa/isort
+    rev: 5.13.2
+    hooks:
+      - id: isort
+        args: ["--profile", "black"]
+  - repo: https://github.com/kynan/nbstripout
+    rev: 0.7.1
+    hooks:
+      - id: nbstripout
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Prevent Commit to Main Branch
+        args: ["--branch", "main"]
+        stages: [pre-commit]

Diff for: README.rst

@@ -11,7 +11,7 @@ PDFgui
 Graphical user interface program for structure refinements to atomic
 pair distribution function.
 
-PDFgui is a friendly interface to PDFfit2 refinement engine, with many
+PDFgui is a friendly interface to the PDFfit2 refinement engine, with many
 powerful extensions.  To get started, please open the manual from the
 help menu and follow the tutorial instructions.  A detailed description
 is available in the doc/Farrow-jpcm-2007.pdf paper.

Diff for: conda-recipe/expandpdfguibase.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python
 
 import sys
+
 from pkg_resources import Requirement, resource_filename
 
 pkg = Requirement.parse("diffpy.pdfgui")

Diff for: devutils/makesdist

@@ -1,51 +1,57 @@
 #!/usr/bin/env python
 
-'''Create source distribution tar.gz archive, where each file belongs
+"""Create source distribution tar.gz archive, where each file belongs
 to a root user and modification time is set to the git commit time.
-'''
+"""
 
-import sys
+import glob
+import gzip
 import os
 import subprocess
-import glob
+import sys
 import tarfile
-import gzip
 
 BASEDIR = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 sys.path.insert(0, BASEDIR)
 
-from setup import versiondata, FALLBACK_VERSION
-timestamp = versiondata.getint('DEFAULT', 'timestamp')
+from setup import FALLBACK_VERSION, versiondata
 
-vfb = versiondata.get('DEFAULT', 'version').split('.post')[0] + '.post0'
+timestamp = versiondata.getint("DEFAULT", "timestamp")
+
+vfb = versiondata.get("DEFAULT", "version").split(".post")[0] + ".post0"
 emsg = "Invalid FALLBACK_VERSION. Expected %r got %r."
 assert vfb == FALLBACK_VERSION, emsg % (vfb, FALLBACK_VERSION)
 
+
 def inform(s):
     sys.stdout.write(s)
     sys.stdout.flush()
     return
 
+
 inform('Run "setup.py sdist --formats=tar" ')
-cmd_sdist = [sys.executable] + 'setup.py sdist --formats=tar'.split()
-ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, 'w'))
-if ec:  sys.exit(ec)
+cmd_sdist = [sys.executable] + "setup.py sdist --formats=tar".split()
+ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, "w"))
+if ec:
+    sys.exit(ec)
 inform("[done]\n")
 
-tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
+tarname = max(glob.glob(BASEDIR + "/dist/*.tar"), key=os.path.getmtime)
 
 tfin = tarfile.open(tarname)
-fpout = gzip.GzipFile(tarname + '.gz', 'w', mtime=0)
-tfout = tarfile.open(fileobj=fpout, mode='w')
+fpout = gzip.GzipFile(tarname + ".gz", "w", mtime=0)
+tfout = tarfile.open(fileobj=fpout, mode="w")
+
 
 def fixtarinfo(tinfo):
     tinfo.uid = tinfo.gid = 0
-    tinfo.uname = tinfo.gname = 'root'
+    tinfo.uname = tinfo.gname = "root"
     tinfo.mtime = timestamp
     tinfo.mode &= ~0o022
     return tinfo
 
-inform('Filter %s --> %s.gz ' % (2 * (os.path.basename(tarname),)))
+
+inform("Filter %s --> %s.gz " % (2 * (os.path.basename(tarname),)))
 for ti in tfin:
     tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
 

Diff for: pyproject.toml

@@ -0,0 +1,22 @@
+[tool.black]
+line-length = 115
+include = '\.pyi?$'
+exclude = '''
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | \.rst
+  | \.txt
+  | _build
+  | buck-out
+  | build
+  | dist
+
+  # The following are specific to Black, you probably don't want those.
+  | blib2to3
+  | tests/data
+)/
+'''

Diff for: requirements/run.txt

@@ -0,0 +1,5 @@
+numpy=1
+wxpython
+diffpy.pdffit2
+diffpy.utils
+matplotlib-base

Diff for: requirements/test.txt

@@ -0,0 +1,2 @@
+pytest
+freezegun

Diff for: setup.py

@@ -11,7 +11,8 @@
 import os
 import re
 import sys
-from setuptools import setup, find_packages
+
+from setuptools import find_packages, setup
 
 # Use this version when git data are not available, like in git zip archive.
 # Update when tagging a new release.
@@ -28,7 +29,7 @@
 
 
 def gitinfo():
-    from subprocess import Popen, PIPE
+    from subprocess import PIPE, Popen
 
     kw = dict(stdout=PIPE, cwd=MYDIR, universal_newlines=True)
     proc = Popen(["git", "describe", "--tags", "--match=v[[:digit:]]*"], **kw)
@@ -67,10 +68,7 @@ def getversioncfg():
     cp = RawConfigParser()
     cp.read(versioncfgfile)
     d = cp.defaults()
-    rewrite = not d or (
-        g["commit"]
-        and (g["version"] != d.get("version") or g["commit"] != d.get("commit"))
-    )
+    rewrite = not d or (g["commit"] and (g["version"] != d.get("version") or g["commit"] != d.get("commit")))
     if rewrite:
         cp.set("DEFAULT", "version", g["version"])
         cp.set("DEFAULT", "commit", g["commit"])

Diff for: src/diffpy/pdfgui/applications/pdfgui.py

@@ -34,9 +34,9 @@
 
 from __future__ import print_function
 
-import sys
-import os
 import getopt
+import os
+import sys
 
 
 def usage():

Diff for: src/diffpy/pdfgui/control/calculation.py

@@ -19,11 +19,13 @@
 import copy
 import math
 
-from diffpy.pdfgui.control.controlerrors import ControlConfigError
-from diffpy.pdfgui.control.controlerrors import ControlKeyError
-from diffpy.pdfgui.control.controlerrors import ControlValueError
+from diffpy.pdfgui.control.controlerrors import (
+    ControlConfigError,
+    ControlKeyError,
+    ControlValueError,
+)
 from diffpy.pdfgui.control.pdfcomponent import PDFComponent
-from diffpy.pdfgui.utils import safeCPickleDumps, pickle_loads
+from diffpy.pdfgui.utils import pickle_loads, safeCPickleDumps
 
 
 class Calculation(PDFComponent):

Diff for: src/diffpy/pdfgui/control/constraint.py

@@ -17,8 +17,8 @@
 constraints will be stored in { variable : constraint } dictionary
 """
 
-import re
 import math
+import re
 
 from diffpy.pdfgui.control.controlerrors import ControlSyntaxError
 
@@ -135,9 +135,7 @@ def __setattr__(self, name, value):
             raise ControlSyntaxError(message)
         # few more checks of the formula:
         if newformula.find("**") != -1:
-            emsg = (
-                "invalid constraint formula '{}', " "operator '**' not supported."
-            ).format(newformula)
+            emsg = ("invalid constraint formula '{}', " "operator '**' not supported.").format(newformula)
             raise ControlSyntaxError(emsg)
         # checks checked
         self.__dict__["formula"] = newformula

Diff for: src/diffpy/pdfgui/control/fitdataset.py

@@ -17,11 +17,12 @@
 """
 
 import copy
+
 import numpy
 
-from diffpy.pdfgui.control.pdfdataset import PDFDataSet
-from diffpy.pdfgui.control.parameter import Parameter
 from diffpy.pdfgui.control.controlerrors import ControlStatusError
+from diffpy.pdfgui.control.parameter import Parameter
+from diffpy.pdfgui.control.pdfdataset import PDFDataSet
 
 
 class FitDataSet(PDFDataSet):
@@ -112,9 +113,7 @@ def getYNames(self):
 
         returns list of strings
         """
-        ynames = ["Gobs", "Gcalc", "Gdiff", "Gtrunc", "dGcalc", "crw"] + list(
-            self.constraints.keys()
-        )
+        ynames = ["Gobs", "Gcalc", "Gdiff", "Gtrunc", "dGcalc", "crw"] + list(self.constraints.keys())
         return ynames
 
     def getXNames(self):
@@ -321,10 +320,7 @@ def writeCalcStr(self):
         Gdiff = self.Gdiff
         drcalc = 0.0
         for i in range(len(self.rcalc)):
-            lines.append(
-                "%g %g %.1f %g %g"
-                % (self.rcalc[i], self.Gcalc[i], drcalc, self.dGcalc[i], Gdiff[i])
-            )
+            lines.append("%g %g %.1f %g %g" % (self.rcalc[i], self.Gcalc[i], drcalc, self.dGcalc[i], Gdiff[i]))
         # lines are ready here
         datastring = "\n".join(lines) + "\n"
         return datastring
@@ -636,9 +632,7 @@ def _set_fitrmin(self, value):
         self._fitrmin = float(value)
         return
 
-    fitrmin = property(
-        _get_fitrmin, _set_fitrmin, doc="Lower boundary for simulated PDF curve."
-    )
+    fitrmin = property(_get_fitrmin, _set_fitrmin, doc="Lower boundary for simulated PDF curve.")
 
     # fitrmax
 
@@ -650,9 +644,7 @@ def _set_fitrmax(self, value):
         self._fitrmax = float(value)
         return
 
-    fitrmax = property(
-        _get_fitrmax, _set_fitrmax, doc="Upper boundary for simulated PDF curve."
-    )
+    fitrmax = property(_get_fitrmax, _set_fitrmax, doc="Upper boundary for simulated PDF curve.")
 
     # fitrstep
 
@@ -664,9 +656,7 @@ def _set_fitrstep(self, value):
         self._fitrstep = float(value)
         return
 
-    fitrstep = property(
-        _get_fitrstep, _set_fitrstep, doc="R-step used for simulated PDF curve."
-    )
+    fitrstep = property(_get_fitrstep, _set_fitrstep, doc="R-step used for simulated PDF curve.")
 
     # rcalc
 
@@ -707,9 +697,7 @@ def _set_dGcalc(self, value):
         self._dGcalc = value
         return
 
-    dGcalc = property(
-        _get_dGcalc, _set_dGcalc, doc="List of standard deviations of Gcalc."
-    )
+    dGcalc = property(_get_dGcalc, _set_dGcalc, doc="List of standard deviations of Gcalc.")
 
     # Gtrunc
 
@@ -757,9 +745,7 @@ def _get_Gdiff(self):
             rv = []
         return rv
 
-    Gdiff = property(
-        _get_Gdiff, doc="Difference between observed and calculated PDF on rcalc grid."
-    )
+    Gdiff = property(_get_Gdiff, doc="Difference between observed and calculated PDF on rcalc grid.")
 
     # crw
     def _get_crw(self):