Changeset 5288

Timestamp:

May 25, 2022 6:12:19 PM (19 months ago)

Author:

toby

Message:

add routines to install gsl and/or diffpy.pdffit2, possibly in a separate environment; add more binaries to the libraries

Location:

trunk

Files:

• GSASIIpath.py (modified) (7 diffs)
• GSASIIphsGUI.py (modified) (5 diffs)
• GSASIIpwd.py (modified) (1 diff)
• docs/source/packages.rst (modified) (2 diffs)

trunk/GSASIIpath.py

@@ -48 +48 @@
     
     :param str key: a value to be found in the configuration (config.py) file
-    :param default: a value to be supplied is none is in the config file or
+    :param default: a value to be supplied if none is in the config file or
       the config file is not found. Defaults to None
     :returns: the value found or the default.
@@ -1327 +1327 @@
         sys.exit()
         
-def condaTest():
+def condaTest(requireAPI=False):
     '''Returns True if it appears that Python is being run under Anaconda 
     Python with conda present. Tests for conda environment vars and that 
@@ -1335 +1335 @@
     '''    
     if not all([(i in os.environ) for i in ('CONDA_DEFAULT_ENV','CONDA_EXE', 'CONDA_PREFIX', 'CONDA_PYTHON_EXE')]): return False
-    # is the conda package available?
-    try:
-        import conda.cli.python_api
-    except:
-        print('You do not have the conda package installed in this environment',
+    if requireAPI:
+        # is the conda package available?
+        try:
+            import conda.cli.python_api
+        except:
+            print('You do not have the conda package installed in this environment',
                   '\nConsider using the "conda install conda" command')
-        return False
+            return False
 
     # There is no foolproof way to check if someone activates conda
@@ -1357 +1358 @@
     # python we are running in shares the beginning part of its path with
     # the one in the base installation:
-    return commonPath(os.environ['CONDA_PYTHON_EXE'],sys.executable)
+    dir1 = os.path.dirname(os.environ['CONDA_PYTHON_EXE'])
+    dir2 = os.path.dirname(sys.executable)
+    if sys.platform != "win32": # python in .../bin/..
+        dir1 = os.path.dirname(dir1)
+        dir2 = os.path.dirname(dir2)    
+    return commonPath(dir1,dir2)
 
 def condaInstall(packageList):
@@ -1375 +1381 @@
       if it did not.
     '''
-    import conda.cli.python_api
+    try:
+        import conda.cli.python_api
+    except:
+        print('You do not have the conda package installed in this environment',
+                  '\nConsider using the "conda install conda" command')
+        return None
     try:
         (out, err, rc) = conda.cli.python_api.run_command(
@@ -1405 +1416 @@
     return out
 
-def commonPath(file1,file2):
-    '''Check if two files share the same path. Note that paths 
-    are considered the same if either file is in a subdirectory 
+def commonPath(dir1,dir2):
+    '''Check if two directories share a path. Note that paths 
+    are considered the same if either directory is a subdirectory 
     of the other, but not if they are in different subdirectories
-    /a/b/c/x.x and  /a/b/c/y.y share a path, as does  /a/b/c/d/y.y
-    but  /a/b/c/d/x.x and  /a/b/c/e/x.x do not.
+    /a/b/c shares a path with /a/b/c/d but /a/b/c/d and /a/b/c/e do not.
 
     :returns: True if the paths are common
     '''
 
-    for i,j in zip(fullsplit(os.environ['CONDA_PYTHON_EXE']),
-               fullsplit(sys.executable)):
+    for i,j in zip(fullsplit(dir1),fullsplit(dir2)):
         if i != j: return False
     return True
@@ -1443 +1452 @@
     return None
     
+def condaEnvCreate(envname, packageList, force=False):
+    '''Create a Python interpreter in a new conda environment. Use this
+    when there is a potential conflict between packages and it would 
+    be better to keep the packages separate (which is one of the reasons
+    conda supports environments). Note that conda should be run from the 
+    case environment; this attempts to deal with issues if it is not. 
+
+    :param str envname: the name of the environment to be created. 
+      If the environment exists, it will be overwritten only if force is True.
+    :param list packageList: a list of conda install create command 
+      options, such as::
+
+            ['python=3.7', 'conda', 'gsl', 'diffpy.pdffit2',
+                '-c', 'conda-forge', '-c', 'diffpy']
+
+    :param bool force: if False (default) an error will be generated 
+      if an environment exists
+
+    :returns: (status,msg) where status is True if an error occurs and
+      msg is a string with error information if status is True or the 
+      location of the newly-created Python interpreter.
+    '''
+    if not all([(i in os.environ) for i in ('CONDA_DEFAULT_ENV',
+                            'CONDA_EXE', 'CONDA_PREFIX', 'CONDA_PYTHON_EXE')]):
+        return True,'not running under conda?'
+    try:
+        import conda.cli.python_api
+    except:
+        return True,'conda package not available (in environment)'
+    # workaround for bug that avoids nesting packages if running from an
+    # environment (see https://github.com/conda/conda/issues/11493)
+    p = os.path.dirname(os.path.dirname(os.environ['CONDA_EXE']))
+    if not os.path.exists(os.path.join(p,'envs')):
+        msg = ('Error derived installation path not found: '+
+                  os.path.join(p,'envs'))
+        print(msg)
+        return True,msg
+    newenv = os.path.join(p,'envs',envname)
+    if os.path.exists(newenv) and not force:
+        msg = 'path '+newenv+' already exists and force is not set, aborting'
+        print(msg)
+        return True,msg
+    pathList = ['-p',newenv]
+    try:
+        (out, err, rc) = conda.cli.python_api.run_command(
+            conda.cli.python_api.Commands.CREATE,
+            packageList + pathList,
+    use_exception_handler=True, stdout=sys.stdout, stderr=sys.stderr
+            )
+        #print('rc=',rc)
+        #print('out=',out)
+        #print('err=',err)
+        if rc != 0: return True,str(out)
+        if sys.platform == "win32":
+            newpython = os.path.join(newenv,'python.exe')
+        else:
+            newpython = os.path.join(newenv,'bin','python')
+        if os.path.exists(newpython):
+            return False,newpython
+        return True,'Unexpected, '+newpython+' not found'
+    except Exception as msg:
+        print("Error occurred, see below\n",msg)
+        return True,'Error: '+str(msg)
+    
+def addCondaPkg():
+    '''Install the conda API into the current conda environment using the 
+    command line, so that the API can be used in the current Python interpreter
+
+    Attempts to do this without a shell failed on the Mac because it seems that
+    the environment was inherited; seems to work w/o shell on Windows. 
+    '''
+    if not all([(i in os.environ) for i in ('CONDA_DEFAULT_ENV','CONDA_EXE',
+                        'CONDA_PREFIX', 'CONDA_PYTHON_EXE')]):
+        return None
+    condaexe = os.environ['CONDA_EXE']
+    currenv = os.environ['CONDA_DEFAULT_ENV']
+    if sys.platform == "win32":
+        cmd = [os.environ['CONDA_EXE'],'install','conda','-n',currenv,'-y']
+        p = subprocess.Popen(cmd,
+                         #stdout=subprocess.PIPE,
+                         stderr=subprocess.PIPE)
+    else:
+        script = 'source ' + os.path.join(
+            os.path.dirname(os.environ['CONDA_PYTHON_EXE']),
+            'activate') + ' base; '
+        script += 'conda install conda -n '+currenv+' -y'
+        p = subprocess.Popen(script,shell=True,env={},
+                         #stdout=subprocess.PIPE,
+                         stderr=subprocess.PIPE)
+    out,err = MakeByte2str(p.communicate())
+    #print('Output from adding conda:\n',out)
+    if err:
+        print('Note error/warning:')
+        print(err)
+    if currenv == "base":
+        print('\nUnexpected action: adding conda to base environment???')
+
 if __name__ == '__main__':
     '''What follows is called to update (or downdate) GSAS-II in a separate process. 

trunk/GSASIIphsGUI.py

@@ -91 +91 @@
 acosd = lambda x: 180.*np.arccos(x)/np.pi
 atan2d = lambda x,y: 180.*np.arctan2(y,x)/np.pi
+is_exe = lambda fpath: os.path.isfile(fpath) and os.access(fpath, os.X_OK)
 
 # previous rigid body selections
@@ -14599 +14600 @@
     # See if if we can import the GSAS-II supplied PDFfit
     pdffitloc = os.path.join(GSASIIpath.path2GSAS2,'PDFfit2')
+    print(pdffitloc,'\n',GSASIIpath.binaryPath)
     if pdffitloc not in sys.path: sys.path.append(pdffitloc)
     try:
@@ -14606 +14608 @@
     except Exception as err:
         pass
-        #print('Failed to import PDFfit2 with error\n:'+str(err))
+        #print('Failed to import PDFfit2 with error:\n'+str(err))
     
     if not os.path.exists(pdffitloc):
         print('PDFfit2 not found in GSAS-II \n\t(expected in '+pdffitloc+')')
         return False
+
     import glob
-    if not glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*')):
-        msg = 'GSAS-II does not supply PDFfit2 for the version of Python that you are using'
-        G2G.G2MessageBox(G2frame,msg,'Need PDFfit2')
+    # see if we can fix things so the GSAS-II version can be used
+    if not GSASIIpath.condaTest() and glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*')):
+        msg = ('GSAS-II supplies a version of PDFfit2 that should be compatible with '+
+        'this Python installation. Since Python was not installed under conda you need '+
+        'to correct this for yourself. You likely need to '+
+        'install GSL (GNU Software Library).')
+        G2G.G2MessageBox(G2frame,msg,'PDFfit2 will not load; No conda')
         return False
-
-    # see if we can fix things so the GSAS-II version can be used
-    if not GSASIIpath.condaTest():
-        msg = ('PDFfit2 is not running with this Python installation. '+
-        'Since Python was not installed under conda you need to install this yourself. '+
-        'pip install diffpy.pdffit2" may do this for you. You will likely need to '+
-        'install the GSL (GNU Software Library).')
-        G2G.G2MessageBox(G2frame,msg,'No conda')
+    elif not GSASIIpath.condaTest():
+        msg = ('GSAS-II does not supply a version of PDFfit2 compatible with '+
+        'this Python installation. Since Python was not installed under conda you need '+
+        'to correct this for yourself. You likely need to '+
+        'install the GSL (GNU Software Library) and use "pip install diffpy.pdffit2".')
+        G2G.G2MessageBox(G2frame,msg,'PDFfit2 not provided; No conda')
         return False
-    # can we access conda?
-    try:
+
+    try:     # have conda. Can we access it programmatically?
         import conda.cli.python_api
     except:
-        msg = ('You do not have the conda package installed in this '+
-                'environment so nothing can be installed.',
-                '\n\nConsider using the "conda install conda" command')
-        G2G.G2MessageBox(G2frame,msg,'conda import error')
-        return False
-    
+        if not glob.glob(os.path.join(GSASIIpath.binaryPath,'pdffit*')):
+            msg = 'GSAS-II does not supply PDFfit2 for the version of Python that you are using'
+        else:
+            msg = 'GSAS-II supplies PDFfit2 that should be compatible with the version of Python that you are using. The problem is likely that the GSL package needs to be installed.'
+        msg += ('\n\nYou do not have the conda package installed in this '+
+                    'environment. This is needed for GSAS-II to install software.'+
+                    '\n\nDo you want to have conda installed for you?')
+        dlg = wx.MessageDialog(G2frame,msg,caption='Install?',
+                                   style=wx.YES_NO|wx.ICON_QUESTION)
+        if dlg.ShowModal() != wx.ID_YES:
+            dlg.Destroy()
+            return False
+        dlg.Destroy()
+        try:
+            wx.BeginBusyCursor()
+            print('Preparing to install conda. This may take a few minutes...')
+            GSASIIpath.addCondaPkg()
+        finally:
+            wx.EndBusyCursor()
+        try:     # have conda. Can we access it programmatically?
+            import conda.cli.python_api
+        except:
+            print('command line conda install did not provide package. Unexpected!')
+            return False
+        
     if 'gsl' not in conda.cli.python_api.run_command(conda.cli.python_api.Commands.LIST,'gsl')[0].lower():
         msg = ('The gsl (GNU Software Library), needed by PDFfit2, '+
@@ -14644 +14668 @@
             return False
         dlg.Destroy()
-        wx.BeginBusyCursor()
-        print('Preparing to install gsl. This may take a few minutes...')
-        res = GSASIIpath.condaInstall(['gsl'])
-        wx.EndBusyCursor()
+
+        try:
+            wx.BeginBusyCursor()
+            print('Preparing to install gsl. This may take a few minutes...')
+            res = GSASIIpath.condaInstall(['gsl','-c','conda-forge'])
+        finally:
+            wx.EndBusyCursor()
         if res:
             msg = 'Installation of the GSL package failed with error:\n' + str(res)
@@ -14657 +14684 @@
         from diffpy.pdffit2 import PdfFit
         #pf = PdfFit()
+        return True
     except Exception as err:
-        msg = 'Failed to import PDFfit2 with error\n:'+str(err)
+        msg = 'Failed to import PDFfit2 with error:\n'+str(err)
         G2G.G2MessageBox(G2frame,msg,'PDFfit2 import error')
+
+    # can we install pdffit2 into our current environment?
+    msg = ('Do you want to try using conda to install PDFfit2 into the '+
+                'current Python (conda) environment, freezing the current '+
+               'configuration? (There is a low chance for success with this.)'+
+               ' The alternative is to install PDFfit2 in a separate environment.'+
+               ' This will be offered next')
+    dlg = wx.MessageDialog(G2frame,msg,caption='Install?',
+                                   style=wx.YES_NO|wx.ICON_QUESTION)
+    if dlg.ShowModal() == wx.ID_YES:
+        try:
+            wx.BeginBusyCursor()
+            print('Preparing to install diffpy.pdffit. This may take a few minutes...')
+            res = GSASIIpath.condaInstall(['diffpy.pdffit2','gsl',
+                                        '-c','diffpy','-c','conda-forge',
+                                           '--freeze-installed'])
+        finally:
+            wx.EndBusyCursor()
+        try: # PDFfit now runs?
+            from diffpy.pdffit2 import PdfFit
+            #pf = PdfFit()
+            return True
+        except Exception as err:
+            msg = 'Failed to import PDFfit2 with error:\n'+str(err)
+            print(msg)
+
+    # Last effort: With conda we should be able to create a separate Python in a separate
+    # environment
+    msg = ('Do you want to try using conda to install PDFfit2 into a separate environment? '+
+               '\n\nIf successful, the pdffit2_exec configuration option will be set to the '+
+               'this new Python environment.')
+    dlg = wx.MessageDialog(G2frame,msg,caption='Install?',
+                                   style=wx.YES_NO|wx.ICON_QUESTION)
+    if dlg.ShowModal() != wx.ID_YES:
         return False
-    return True
+    try:
+        wx.BeginBusyCursor()
+        print('Preparing to create a conda environment. This may take a few minutes...')
+        res,PDFpython = GSASIIpath.condaEnvCreate('pdffit2',
+                    ['python=3.7', 'conda', 'gsl', 'diffpy.pdffit2',
+                         '-c', 'conda-forge', '-c', 'diffpy'])
+    finally:
+        wx.EndBusyCursor()
+    if os.path.exists(PDFpython):
+        vars = G2G.GetConfigValsDocs()
+        vars['pdffit2_exec'][1] = PDFpython
+        GSASIIpath.SetConfigValue(vars)
+        G2G.SaveConfigVars(vars)
+        print('config',GSASIIpath.GetConfigValue('pdffit2_exec'))
+        return True
+    else:
+        msg = 'Failed to install PDFfit2 with error:\n'+str(PDFpython)
+        print(msg)
+        G2G.G2MessageBox(G2frame,
+            'Install failed. See console for error message\n\n'+
+            'All attempts to install PDFfit2 have failed. '+
+            'Do you have write access to where GSAS-II is installed?',
+            'PDFfit2 install error')
+        return False

trunk/GSASIIpwd.py

@@ -3330 +3330 @@
     PDFfit_exe,PDFfit_path = findPDFfit()  # returns python loc and path(s) for pdffit
     if not PDFfit_exe:
-        GSASIIpath.IPyBreak()
-        return None
-    for p in PDFfit_path:
-        rundata += "sys.path.append(r'{:}')\n".format(p)
+        print('PDFfit2 is not found. Creating .sh file without paths.')
+    if PDFfit_path:
+        for p in PDFfit_path:
+            rundata += "sys.path.append(r'{:}')\n".format(p)
     rundata += 'from diffpy.pdffit2 import PdfFit\n'
     rundata += 'pf = PdfFit()\n'

trunk/docs/source/packages.rst

@@ -61 +61 @@
   GSAS-II to download updates to our code. This can be skipped if svn
   is installed directly (easy Linux, but a bit harder on MacOS and
-  Windows).
+  Windows). In conda-forge this package is called subversion, but at
+  present is only available for Linux.
+* pywin32 (windows only): this provides the win32com module that is
+  used to install GSAS-II on windows machines. GSAS-II can be used on
+  Windows without this, but the installation will offer less
+  integration into Windows. 
 * conda: the conda package allows access to conda features from
   inside Python. It will be used inceasingly by GSAS-II to
@@ -73 +78 @@
   Python interpreter::
 
-    conda install wxpython numpy scipy matplotlib pyopengl pillow h5py imageio svn -c conda-forge
-    
-  or to use a separate environment (here named ``g2python``), use::
-
-    conda install -n g2python wxpython numpy scipy matplotlib pyopengl pillow h5py imageio svn conda -c conda-forge
-
+    conda install python=3.9 wxpython numpy scipy matplotlib pyopengl pillow h5py imageio subversion -c conda-forge
+    
+  or to put a Python configured for GSAS-II into a separate conda
+  environment (here named ``g2python``, but any name can be used), use
+  command::
+
+    conda create -n g2python python=3.9 wxpython numpy scipy matplotlib pyopengl  pillow h5py imageio conda subversion -c conda-forge 
+
+Note that at present the subversion is only available for Linux, so
+that should be removed from the commands above. For windows add pywin32
+Also, while there is no
+reason why GSAS-II should not run with Python 3.10, we are not yet
+providing binaries for this. 
+   
 Remember to activate using: ``<path>\Scripts\activate``  (windows); 
 ``source <path>/bin/activate`` (Mac/Linux). Note that one should add