documentation, blog, update module list

_doc/sphinxdoc/source/blog/2015/2015-09-19_mako.rst

@@ -3,7 +3,7 @@
 .. blogpost::
     :title: Warning with Mako
     :keywords: Mako, warning, issue
-    :date: 2015-09-17
+    :date: 2015-09-19
     :categories: install, modules, issue
 
     The installation of `Mako <http://www.makotemplates.org/>`_

_doc/sphinxdoc/source/blog/2015/2015-09-20_cvxpy.rst

@@ -0,0 +1,13 @@
+
+
+.. blogpost::
+    :title: Install cvxpy on Windows
+    :keywords: cvxpy, Windows
+    :date: 2015-09-20
+    :categories: install, modules, issue
+
+    After I installed `CVXcanon <https://github.com/cvxgrp/CVXcanon>`_ (see previous blog), 
+    I went through an issue
+    ``canonInterface`` is not found.
+    I corrected with the following modification:
+    `change import instruction to use CVXcanon explicitely  <https://github.com/sdpython/cvxpy/commit/11fe2bff21cbafcb694cab1265f111e6f9314ac4>`_.

src/pymyinstall/packaged/packaged_config_1_small.py

@@ -109,6 +109,8 @@ def small_set():
         ModuleInstall('markupsafe', 'pip', purpose="parses mardown"),
         ModuleInstall(
             "pandas", "wheel", purpose="manipulate table as SQL in memory", usage="DATA/ML"),
+        ModuleInstall(
+            "pandas-datareader", "pip", purpose="Up to date remote data access for pandas, works for multiple versions of pandas.", usage="DATA/ML"),
         ModuleInstall(
             "netCDF4", "wheel", mname="netCDF4", purpose="xray uses this module to save and read data (netCDF=Unidata network Common Data Form)"),
         ModuleInstall(

src/pymyinstall/packaged/packaged_config_3_extended.py

@@ -90,7 +90,7 @@ def extended_set():
         ModuleInstall(
             'lockfile', 'pip', purpose="Platform-independent file locking module"),
         ModuleInstall('python-daemon', 'pip', mname="daemon",
-                      purpose="Library to implement a well-behaved Unix daemon process (for luigi)"),
+                      purpose="Library to implement a well-behaved Unix daemon process (for luigi)") if not sys.platform.startswith("win") else None,
         ModuleInstall('cached_property', 'pip',
                       purpose="A decorator for caching properties in classes (for luigi)"),
         ModuleInstall('luigi', 'pip',
@@ -156,8 +156,8 @@ def extended_set():
             "ecos", "wheel", purpose="ECOS is a numerical software for solving convex second-order cone programs (SOCPs)", usage="OPTIM"),
         ModuleInstall(
             "CVXcanon", "wheel_xd", purpose="A low-level library to perform the matrix building step in cvxpy, a convex optimization modeling software.", usage="OPTIM"),
-        ModuleInstall(
-            "cvxpy", "pip", purpose="linear, quadratic optimization, depends on cvxopt", usage="OPTIM"),
+        ModuleInstall("cvxpy", "github", "sdpython", usage="OPTIM",
+                      purpose="linear, quadratic optimization, depends on cvxopt"),
         # better large list
         ModuleInstall(
             "blist", "wheel", purpose="a list-like type with better asymptotic performance and similar performance on small lists"),
@@ -182,7 +182,9 @@ def extended_set():
             "Theano", "wheel", mname="theano", purpose="deep learning, GPU", usage="DATA/ML"),
         ModuleInstall('pymc', 'wheel',
                       purpose="Monte Carlo computation", usage="DATA/ML"),
-        ModuleInstall('pymc', 'wheel', web="https://github.com/pymc-devs/pymc3",
+        ModuleInstall('pymc', 'wheel', web="https://github.com/pymc-devs/pymc",
+                      purpose="Monte Carlo computation", usage="DATA/ML") if sys.version_info[0] >= 3 else None,
+        ModuleInstall('pymc3', 'github', "pymc-devs", web="https://github.com/pymc-devs/pymc3",
                       purpose="Monte Carlo computation (Python 3 only)", usage="DATA/ML") if sys.version_info[0] >= 3 else None,
         ModuleInstall('pysterior', 'pip',
                       purpose="pysterior is a machine learning library for Python which aims to make Bayesian parametric regression and classification models accessible and easy to use. The library allows users to construct supervised learning models using an intuitive interface similar to that used by scikit-learn.", usage="DATA/ML") if sys.version_info[0] >= 3 else None,
@@ -229,7 +231,7 @@ def extended_set():
             "locket", "pip",
             purpose="File-based locks for Python for Linux and Windows"),
         ModuleInstall(
-            "dill", "pip", purpose="serialize all of python (almost), Dill extends python's \"pickle\" module for serializing and de-serializing python objects to the majority of the built-in python types."),  # for dask
+            "dill", "pip", purpose="serialize all of python (almost), Dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types."),  # for dask
         # parallel computation
         ModuleInstall(
             "dask", "pip", purpose="parallization of operations with dataframe", usage="DATA/ML"),

src/pymyinstall/packaged/packaged_config_4_ml.py

@@ -288,18 +288,19 @@ def ensae_set():
         # purpose="Turn your Python and Javascript code into DOT flowcharts"),
 
         # biokit
+        ModuleInstall("wrapt", "wheel",
+                      purpose="A Python module for decorators, wrappers and monkey patching."),
         ModuleInstall("colormap", "pip", usage="VIZ",
                       purpose="Utilities to ease manipulation of matplotlib colormaps and color codecs (e.g., hex2rgb)"),
         ModuleInstall("easydev", "pip",
                       purpose="Common utilities to ease the development of Python packages"),
         ModuleInstall("suds-jurko", "pip", mname="suds",
                       purpose="Lightweight SOAP client (Jurko's fork)"),
-        ModuleInstall("wrapt", "wheel",
-                      purpose="A Python module for decorators, wrappers and monkey patching."),
-        ModuleInstall("bioservices", "pip",
-                      purpose="Access to Biological Web Services from Python"),
-        ModuleInstall("biokit", "github", "biokit", usage="VIZ",
-                      purpose="Access to Biological Web Services from Python"),
+        # bugged and still uses ordereddict
+        # ModuleInstall("bioservices", "pip",
+        #              purpose="Access to Biological Web Services from Python"),
+        # ModuleInstall("biokit", "github", "biokit", usage="VIZ",
+        # purpose="Access to Biological Web Services from Python"),
 
 
         # azure part

src/pymyinstall/win_installer/win_setup_main.py

@@ -499,7 +499,8 @@ def last_function(inno_script, folders, verbose=False, fLOG=print):
         #########
         # checking
         #########
-        distribution_checkings(folders["python"], folders["tools"], fLOG=fLOG)
+        distribution_checkings(folders["python"], folders[
+                               "tools"], fLOG=fLOG, module_list=module_list)
 
     ########
     # tutorial

src/pymyinstall/win_installer/win_setup_main_checkings.py

@@ -20,14 +20,15 @@
     FileNotFoundError = Exception
 
 
-def distribution_checkings(python_path, tools_path, fLOG=print, skip_import=False):
+def distribution_checkings(python_path, tools_path, fLOG=print, skip_import=False, module_list=None):
     """
     checks a distribution was properly executed
 
     @param      python_path     path for python
     @param      tools_path      path for tools
     @param      fLOG            logging function
     @param      skip_import     skip the validation of every installed module (for unit test purposes)
+    @param      module_list     module list to check
 
     The function raises @see cl WinInstallDistributionError if an issue is detected.
 
@@ -66,7 +67,7 @@ def distribution_checkings(python_path, tools_path, fLOG=print, skip_import=Fals
     ################################
     if not skip_import:
         res = import_every_module(
-            python_path, None, only_installed=True, fLOG=fLOG)
+            python_path, module_list, only_installed=True, fLOG=fLOG)
         mes = []
         for r in res:
             if not r[0]:
@@ -114,11 +115,13 @@ def tomod(m):
 
     def noLOG(*l, **p):
         pass
-        
+
     def is_errored_line(line):
         if ".py" in line:
             if "UserWarning:" in line:
                 return False
+            if "FutureWarning:" in line:
+                return False
             return True
         return False
 
@@ -132,12 +135,7 @@ def analyze_error_success(mod, err):
         if "kivy" in mod.name.lower():
             if "error" not in err.lower():
                 return True
-
-        if mod.name in {"simplepam", "ordereddict"
-                }:
-            # these modules should not be used
-            return False
-
+
         if err is not None:
             lines = err.split("\n")
             for line in lines:
@@ -181,7 +179,8 @@ def analyze_error_success(mod, err):
                 fLOG("{0}/{1}: success".format(i, len(module_list)), m)
             else:
                 fLOG("{0}/{1}: failed ".format(i, len(module_list)), m)
-                err = [ (" - ERR: " if is_errored_line(line) else " - OK:  ") + line for line in err.split("\n") ]
+                err = [(" - ERR: " if is_errored_line(line)
+                        else " - OK:  ") + line for line in err.split("\n")]
                 err = "\n".join(err)
             res.append((suc, m, out, err))
     return res