Merge pull request #162 from sciris/fixes-jan2021

Release 1.0.1

CHANGELOG.rst

@@ -6,6 +6,26 @@ All notable changes to this project will be documented in this file.
 By import convention, components of the Sciris library are listed beginning with ``sc.``, e.g. ``sc.odict()``.
 
 
+Version 1.0.1 (2021-03-01)
+---------------------------
+1. Fixed bug with Matplotlib 3.4.0 also defining colormap ``'turbo'``, which caused Sciris to fail to load.
+2. Added a new function, ``sc.orderlegend()``, that lets you specify the order you want the legend items to appear.
+3. Fixed bug with paths returned by ``sc.getfilelist(nopath=True)``.
+4. Fixed bug with ``sc.loadjson()`` only reading from a string if ``fromfile=False``.
+5. Fixed recursion issue with printing ``sc.Failed`` objects.
+6. Changed ``sc.approx()`` to be an alias to ``np.isclose()``; this function may be removed in future versions.
+7. Changed ``sc.findinds()`` to call ``np.isclose()``, allowing for greater flexibility.
+8. Changed the ``repr`` for ``sc.objdict()`` to differ from ``sc.odict()``.
+9. Improved ``sc.maximize()`` to work on more platforms (but still not inline or on Macs).
+10. Improved the flexiblity of ``sc.htmlify()`` to handle tabs and other kinds of newlines.
+11. Added additional checks to ``sc.prepr()`` to avoid failing on recursive objects.
+12. Updated ``sc.mergedicts()`` to return the same type as the first dict supplied.
+13. Updated ``sc.readdate()`` and ``sc.date()`` to support timestamps as well as strings.
+14. Updated ``sc.gitinfo()`` to try each piece independently, so if it fails on one (e.g., extracting the date) it will still return the other pieces (e.g., the hash).
+15. Pinned ``xlrd`` to 1.2.0 since later versions fail to read xlsx files.
+
+
+
 Version 1.0.0 (2020-11-30)
 --------------------------
 This major update (and official release!) includes many new utilities adopted from the `Covasim <http://covasim.org>`__ and `Atomica <http://atomica.tools>`__ libraries, as well as important improvements and bugfixes for parallel processing, object representation, and file I/O.

sciris/sc_fileio.py

@@ -235,7 +235,7 @@ def getfilelist(folder='.', pattern=None, abspath=False, nopath=False, filesonly
         nopath      (bool): whether to return no path
         filesonly   (bool): whether to only return files (not folders)
         foldersonly (bool): whether to only return folders (not files)
-        recursive   (bool): passd to glob()
+        recursive   (bool): passed to glob()
 
     Returns:
         List of files/folders
@@ -258,7 +258,7 @@ def getfilelist(folder='.', pattern=None, abspath=False, nopath=False, filesonly
     elif foldersonly:
         filelist = [f for f in filelist if os.path.isdir(f)]
     if nopath:
-        filelist = [f[len(folder):] for f in filelist]
+        filelist = [os.path.basename(f) for f in filelist]
     return filelist
 
 
@@ -520,23 +520,23 @@ def loadjson(filename=None, folder=None, string=None, fromfile=True, **kwargs):
     Returns:
         output (dict): the JSON object
 
-    **Example**::
+    **Examples**::
 
         json = sc.loadjson('my-file.json')
+        json = sc.loadjson(string='{"a":null, "b":[1,2,3]}')
     '''
-    if fromfile:
-        filename = makefilepath(filename=filename, folder=folder)
-        try:
-            with open(filename) as f:
-                output = json.load(f, **kwargs)
-        except FileNotFoundError as E:
-            print('Warning: file not found. Use fromfile=False if not loading from a file')
-            raise E
-    else:
+    if string is not None or not fromfile:
         if string is None and filename is not None:
             string = filename # Swap arguments
         output = json.loads(string, **kwargs)
-
+    else:
+        filepath = makefilepath(filename=filename, folder=folder)
+        try:
+            with open(filepath) as f:
+                output = json.load(f, **kwargs)
+        except FileNotFoundError as E:
+            errormsg = f'No such file "{filename}". Use fromfile=False if loading a JSON string rather than a file.'
+            raise FileNotFoundError(errormsg) from E
     return output
 
 
@@ -1093,7 +1093,7 @@ def __init__(self, *args, **kwargs):
         pass
 
     def __repr__(self):
-        output = ut.prepr(self) # This does not include failure_info since it's a class attribute
+        output = ut.objrepr(self) # This does not include failure_info since it's a class attribute
         output += self.showfailures(verbose=False, tostring=True)
         return output
 
@@ -1400,4 +1400,8 @@ def _unpickleMethod(im_name, im_self, im_class):
         bound = types.MethodType(methodFunction, im_self, *maybeClass)
         return bound
 
-cpreg.pickle(types.MethodType, _pickleMethod, _unpickleMethod)
+cpreg.pickle(types.MethodType, _pickleMethod, _unpickleMethod)
+
+# Legacy support for loading Sciris <1.0 objects; may be removed in future
+pickleMethod = _pickleMethod
+unpickleMethod = _unpickleMethod

sciris/sc_math.py

@@ -19,21 +19,25 @@
 __all__ = ['approx', 'safedivide', 'findinds', 'findfirst', 'findlast', 'findnearest', 'dataindex', 'getvalidinds', 'sanitize', 'getvaliddata', 'isprime']
 
 
-def approx(val1=None, val2=None, eps=None):
+def approx(val1=None, val2=None, eps=None, **kwargs):
     '''
-    Determine whether two scalars approximately match.
+    Determine whether two scalars (or an array and a scalar) approximately match.
+    Alias for np.isclose() and may be removed in future versions.
+
+    Args:
+        val1 (number or array): the first value
+        val2 (number): the second value
+        eps (float): absolute tolerance
+        kwargs (dict): passed to np.isclose()
 
     **Examples**::
 
         sc.approx(2*6, 11.9999999, eps=1e-6) # Returns True
         sc.approx([3,12,11.9], 12) # Returns array([False, True, False], dtype=bool)
-
-    Note: in most cases, np.isclose() is preferable.
     '''
-    if val2 is None: val2 = 0.0
-    if eps  is None: eps = 1e-9
-    if isinstance(val1, list): val1 = np.array(val1) # If it's a list, convert to an array first
-    output = abs(val1-val2)<=eps
+    if eps is not None:
+        kwargs['atol'] = eps # Rename kwarg to match np.isclose()
+    output = np.isclose(a=val1, b=val2, **kwargs)
     return output
 
 
@@ -71,26 +75,27 @@ def safedivide(numerator=None, denominator=None, default=None, eps=None, warn=Fa
     return output
 
 
-def findinds(arr, val=None, eps=1e-6, first=False, last=False):
+def findinds(arr, val=None, eps=1e-6, first=False, last=False, **kwargs):
     '''
     Little function to find matches even if two things aren't eactly equal (eg.
     due to floats vs. ints). If one argument, find nonzero values. With two arguments,
     check for equality using eps. Returns a tuple of arrays if val1 is multidimensional,
-    else returns an array.
+    else returns an array. Similar to calling np.nonzero(np.isclose(arr, val)).
 
     Args:
         arr (array): the array to find values in
         val (float): if provided, the value to match
-        eps (float): the precision for matching (default 1e-6)
+        eps (float): the precision for matching (default 1e-6, equivalent to np.isclose's atol)
         first (bool): whether to return the first matching value
         last (bool): whether to return the last matching value
+        kwargs (dict): passed to np.isclose()
 
     **Examples**::
 
         sc.findinds(rand(10)<0.5) # e.g. array([2, 4, 5, 9])
         sc.findinds([2,3,6,3], 6) # e.g. array([2])
 
-    Version: 2020nov29
+    Version: 2021mar01
     '''
 
     # Handle first or last
@@ -102,6 +107,7 @@ def findinds(arr, val=None, eps=1e-6, first=False, last=False):
         ind = -1
     else:
         ind = None
+    atol = kwargs.pop('atol', eps) # Ensure atol isn't specified twice
 
     # Calculate matches
     arr = np.array(arr)
@@ -111,7 +117,7 @@ def findinds(arr, val=None, eps=1e-6, first=False, last=False):
         if ut.isstring(val):
             output = np.nonzero(arr==val)
         else:
-            output = np.nonzero(abs(arr-val)<eps) # If absolute difference between the two values is less than a certain amount
+            output = np.nonzero(np.isclose(a=arr, b=val, atol=atol, **kwargs)) # If absolute difference between the two values is less than a certain amount
 
     # Process output
     if arr.ndim == 1: # Uni-dimensional

sciris/sc_odict.py

@@ -160,7 +160,7 @@ def __setitem__(self, key, value):
         return None
 
 
-    def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthresh=10, numindents=0, recursionlevel=0, sigfigs=None, numformat=None, maxitems=200):
+    def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthresh=10, numindents=0, recursionlevel=0, sigfigs=None, numformat=None, maxitems=200, classname='odict()', quote='"', keysep=':'):
         ''' Print a meaningful representation of the odict '''
 
         # Set primitives for display.
@@ -181,9 +181,9 @@ def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthres
         halfmax = int(maxitems/2)
         extraitems = 0
         if nkeys == 0:
-            output = 'odict()'
+            output = classname
         else:
-            output = '' # Initialize the output to nothing.
+            output = ''
             keystrs = [] # Start with an empty list which we'll save key strings in.
             valstrs = [] # Start with an empty list which we'll save value strings in.
             vallinecounts = [] # Start with an empty list which we'll save line counts in.
@@ -202,7 +202,7 @@ def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthres
                         if recursionlevel <= maxrecursion:
                             thisvalstr = ut.flexstr(thisval.__repr__(maxlen=maxlen, showmultilines=showmultilines, divider=divider, dividerthresh=dividerthresh, numindents=numindents, recursionlevel=recursionlevel+1, sigfigs=sigfigs, numformat=numformat))
                         else:
-                            thisvalstr = 'odict() [maximum recursion reached]'
+                            thisvalstr = f'{classname} [maximum recursion reached]'
                     elif ut.isnumber(thisval): # Flexibly print out numbers, since they're largely why we're here
                         if numformat is not None:
                             thisvalstr = numformat % thisval
@@ -213,7 +213,7 @@ def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthres
                     else: # Otherwise, do the normal repr() read.
                         thisvalstr = repr(thisval)
                 except Exception as E:
-                    thisvalstr = '%s read failed: %s' % (ut.objectid(thisval), str(E))
+                    thisvalstr = f'{ut.objectid(thisval)} read failed: {str(E)}'
 
                 # Add information to the lists to retrace afterwards.
                 keystrs.append(thiskeystr)
@@ -250,9 +250,9 @@ def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthres
                 # Create the the text to add, apply the indent, and add to the output
                 spacer = ' '*(maxkeylen-len(keystr))
                 if vallinecount == 1 or not showmultilines:
-                    rawoutput = '#%i: "%s":%s %s\n' % (ind, keystr, spacer, valstr)
+                    rawoutput = f'#{ind:d}: {quote}{keystr}{quote}{keysep}{spacer} {valstr}\n'
                 else:
-                    rawoutput = '#%i: "%s":%s \n%s\n' % (ind, keystr, spacer, valstr)
+                    rawoutput = f'#{ind:d}: {quote}{keystr}{quote}{keysep}{spacer} \n{valstr}\n'
 
                 # Perform the indentation.
                 newoutput = ut.indent(prefix=theprefix, text=rawoutput, width=80)
@@ -277,9 +277,9 @@ def __repr__(self, maxlen=None, showmultilines=True, divider=False, dividerthres
         return output
 
 
-    def _repr_pretty_(self, p, cycle):
+    def _repr_pretty_(self, p, cycle, *args, **kwargs):
         ''' Function to fix __repr__ in IPython'''
-        print(self.__repr__())
+        print(self.__repr__(*args, **kwargs))
 
 
     def disp(self, maxlen=None, showmultilines=True, divider=False, dividerthresh=10, numindents=0, sigfigs=5, numformat=None):
@@ -863,6 +863,11 @@ class objdict(odict):
     >>> od.keys = 3 # This raises an exception (you can't overwrite the keys() method)
     '''
 
+    def __repr__(self, *args, **kwargs):
+        ''' Use odict repr, but with a custom class name and no quotes '''
+        return super().__repr__(quote='', keysep='.', classname='objdict()', *args, **kwargs)
+
+
     def __getattribute__(self, attr):
         try: # First, try to get the attribute as an attribute
             output = odict.__getattribute__(self, attr)
@@ -886,7 +891,6 @@ def __setattr__(self, name, value):
         errormsg = '"%s" exists as an attribute, so cannot be set as key; use setattribute() instead' % name
         raise Exception(errormsg)
 
-        return None
 
     def setattribute(self, name, value):
         ''' Set attribute if truly desired '''