Merge pull request SimVascular#5 from zasexton/master

4-Adding-importing-functions-for-SV-Python-interpreter

PythonAPI/Importing/README.md

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+ # Tools for Installing, Uninstalling, and Checking for SV Python Packages
+Currently this code serves as a template to be copied into scripts that are
+loaded into the SV Python API Interface when additional Python modules are
+needed but not included within the base SV Python Interpreter. For reference,
+the python modules included with the base SV Python Interpreter can be listed
+from the following command.
+
+```python
+help("modules")
+```
+
+Albeit after much complaining, the SV Python Interpreter will return a
+comprehensive list of all the included modules which are available by
+default. If your script requires a new or different version of one of
+these modules, *be careful*. Changing one of these modules may affect
+performance of internal routines and cause unpredicted behaviors to
+occur. This is especially true for the `vtk` module which is called
+by `sv` specific modules to return PolyData objects. This list of included
+modules is also provided here for reference.
+
+| | | | |
+|:----:|:----:|:---:|:---:|
+|Cython | codeop | netrc | sys|
+|IPython |collections | nntplib | sysconfig|
+|__future__ | colorama | notebook | tabnanny|
+|_ast | colorsys | nt | tarfile|
+|_bisect | commctrl | ntpath | telnetlib|
+|_bootlocale | compileall | ntsecuritycon | tempfile|
+|_cffi_backend | concurrent | nturl2path | tensorboard|
+|_codecs | configparser | numbers | tensorflow|
+|_codecs_cn | contextlib | numpy | tensorflow_estimator|
+|_codecs_hk | copy | odbc | termcolor|
+|_codecs_iso2022 | copyreg | opcode | terminado|
+|_codecs_jp | crypt | operator | testpath|
+|_codecs_kr | csv | optparse | tests|
+|_codecs_tw | ctypes | os | textwrap|
+|_collections | curses | packaging | this|
+|_collections_abc | cycler | pandocfilters | threading|
+|_compat_pickle | cygwin_bash_kernel | parser | time|
+|_compression | cython | parso | timeit|
+|_csv | cythonmagic | pasta | timer|
+|_ctypes | datetime | pathlib | tkinter|
+|_ctypes_test | dateutil | pdb | token|
+|_datetime | dbi | perfmon | tokenize|
+|_decimal | dbm | pickle | tornado|
+|_distutils_hack | dde | pickleshare | trace|
+|_dummy_thread | decimal | pickletools | traceback|
+|_elementtree | decorator | pip | tracemalloc|
+|_functools | defusedxml | pipes | traitlets|
+|_hashlib | difflib | pkg_resources | tty|
+|_heapq | dis | pkgutil | turtle|
+|_imp | distutils | platform | turtledemo|
+|_io | doctest | plistlib | types|
+|_json | dummy_threading | poplib | typing|
+|_locale | easy_install | posixpath | unicodedata|
+|_lsprof | echo_kernel | powershell_kernel | unittest|
+|_markupbase | email | pprint | urllib|
+|_md5 | encodings | profile | urllib3|
+|_msi | ensurepip | prometheus_client | uu|
+|_multibytecodec | entrypoints | prompt_toolkit | uuid|
+|_multiprocessing | enum | pstats | venv|
+|_opcode | errno | pty | vtk|
+|_operator | faulthandler | pvectorc | warnings|
+|_osx_support | filecmp | pwlf | wave|
+|_overlapped | fileinput | pyDOE | wcwidth|
+|_pickle | fnmatch | py_compile | weakref|
+|_pydecimal | formatter | pyclbr | webbrowser|
+|_pyio | fractions | pycparser | webencodings|
+|_pyrsistent_version| ftplib | pydoc | werkzeug|
+|_random | functools | pydoc_data | wheel|
+|_sha1 | gast | pyexpat | widgetsnbextension|
+|_sha256 | gc | pygments | win2kras|
+|_sha512 | genericpath | pyparsing | win32api|
+|_signal | getopt | pyrsistent | win32clipboard|
+|_sitebuiltins | getpass | pythoncom | win32com|
+|_socket | gettext | pywin | win32con|
+|_sqlite3 | glob | pywin32_bootstrap | win32console|
+|_sre | grpc | pywin32_testutil | win32cred|
+|_ssl | gzip | pywintypes | win32crypt|
+|_stat | h5py | pyximport | win32cryptcon|
+|_string | hashlib | qtconsole | win32event|
+|_strptime | heapq | qtpy | win32evtlog|
+|_struct | hmac | queue | win32evtlogutil|
+|_symtable | html | quopri | win32file|
+|_testbuffer | http | random | win32gui|
+|_testcapi | idlelib | rasutil | win32gui_struct|
+|_testimportmultiple| idna | re | win32help|
+|_testmultiphase | imaplib | regcheck | win32inet|
+|_thread | imghdr | regutil | win32inetcon|
+|_threading_local | imp | reprlib | win32job|
+|_tkinter | importlib | requests | win32lz|
+|_tracemalloc | importlib_metadata | rlcompleter | win32net|
+|_warnings | inspect | rmagic | win32netcon|
+|_weakref | io | run | win32pdh|
+|_weakrefset | ipaddress | runpy | win32pdhquery|
+|_win32sysloader | ipykernel | sched | win32pdhutil|
+|_winapi | ipykernel_launcher | scipy | win32pipe|
+|_winxptheme | ipython_genutils | select | win32print|
+|_yaml | ipywidgets | selectors | win32process|
+|abc | isapi | send2trash | win32profile|
+|absl | itertools | servicemanager | win32ras|
+|adodbapi | jedi | setuptools | win32rcparser|
+|afxres | jinja2 | shelve | win32security|
+|aifc | json | shlex | win32service|
+|antigravity | jsonschema | shutil | win32serviceutil|
+|argon2 | jupyter | signal | win32timezone|
+|argparse | jupyter_client | simvascular_python_kernel | win32trace|
+|array | jupyter_console | simvascular_tcl_kernel | win32traceutil|
+|ast | jupyter_core | site | win32transaction|
+|astor | keras_applications | six | win32ts|
+|asynchat | keras_preprocessing| smtpd | win32ui|
+|asyncio | keyword | smtplib | win32uiole|
+|asyncore | kiwisolver | sndhdr | win32verstamp|
+|atexit | lib2to3 | socket | win32wnet|
+|attr | linecache | socketserver | win_unicode_console|
+|audioop | locale | sqlite3 | winerror|
+|autoreload | logging | sre_compile | winioctlcon|
+|backcall | lzma | sre_constants | winnt|
+|base64 | macpath | sre_parse | winperf|
+|bdb | macurl2path | ssl | winpty|
+|binascii | mailbox | sspi | winreg|
+|binhex | mailcap | sspicon | winxpgui|
+|bisect | markdown | stat | winxptheme|
+|bleach | markupsafe | statistics | wrapt|
+|builtins | marshal | storemagic | wsgiref|
+|bz2 | math | string | xdrlib|
+|cProfile | mimetypes | stringprep | xml|
+|calendar | mistune | struct | xmlrpc|
+|certifi | mmap | subprocess | xxsubtype|
+|cffi | mmapfile | sunau | yaml|
+|cgi | mmsystem | sv | zipapp|
+|cgitb | modulefinder | sv_ml | zipfile|
+|chardet | msilib | sv_rom_extract_results | zipimport|
+|chunk | msvcrt | sv_rom_simulation | zipp|
+|cmath | multiprocessing | sv_vis | zlib|
+|cmd | nbconvert | symbol | zmq|
+|code | nbformat | sympyprinting | |
+|codecs | netbios | symtable | |
+
+Again, this is meant to be a convenient list of modules that are most likely
+available with the base SV Python Interpreter; however, this should be confirmed
+on your own machine before assuming that is or is not available.
+
+To check the version of a given module the following code can be run. This may
+be important when checking for potential conflict between SV and external
+package dependencies. If there is a conflict between versions, always prioritize
+the SV package version dependency.
+
+```python
+import pkg_resources
+pkg_resources.get_distribution('<package_name>').version
+```
+
+Example:
+```python
+>>> import pkg_resources
+>>> pkg_resources.get_distribution('six').version
+'1.15.0'
+```
+
+This tool folder contains the `install`, `uninstall`, and `search` functions.
+These functions attempt to find packages and add or remove them to the
+SV Python 3.5.5 Interpreter.
+
+## Help
+
+For more information on function usage, inputs, and return values, run the
+`help(<function_name>)` command on a given function.
+
+```python
+help(install)
+help(uninstall)
+help(search)
+```

PythonAPI/Importing/install.py

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+#!/usr/bin/env python
+
+# author: Zachary Sexton
+# date: 8-31-21
+
+from pip._internal import main as pipmain
+
+def install(package_name,version=None,inequality=None):
+ """
+ Install a python package from within the python SV Interpreter.
+
+ Parameters
+ ----------
+
+ package_name : str
+ python package name for lookup on https://pypi.org/
+ version : str, optional
+ package version to install. Default is None meaning that
+ no constraints on package version will be supplied
+ inequality : str, optional
+ supplied as an additional argument if multiple packages
+ satisfy the desired requirements above or below the given
+ package version specified. By default inequality is None,
+ meaning that the inequality argument is ignored; however
+ if a version is supplied without an accompanying inequality
+ argument then inequality defaults to strict equality '=='
+
+ Accepted string arguments are the following:
+ '==', '<', '>', '<=', '>='
+
+ Returns
+ -------
+
+ success : bool
+ if a package was successfully installed success will be True,
+ otherwise success will return False
+ """
+ # Sanitizing Inputs for package requirements
+ if not isinstance(package_name,str):
+ print('package_name argument must be of type -> str')
+ return False
+ if not isinstance(version,str) and not version is None:
+ print('version argument must be of type -> str')
+ return False
+ if not isinstance(inequality,str) and inequality is not None:
+ print('inequality argument must be of type -> str')
+ return False
+ # Checking logical package constraints (if applicable)
+ if inequality is not None:
+ if inequality is not in ['==','<','>','<=','>=']:
+ print('inequality must be one of the following: == < > <= >=')
+ return False
+ if version is None:
+ print('version must be given if an inequality argument is given')
+ return False
+ # Attempting package fetching and installation
+ try:
+ if version is None:
+ pipmain(['install',package_name])
+ elif version is not None and inequality is None:
+ pipmain(['install',package_name+'=='+version])
+ elif version is not None and inequality is not None:
+ pipmain(['install',package_name+inequality+version])
+ success = True
+ except:
+ print('package installation failed')
+ success = False
+ return success

PythonAPI/Importing/uninstall.py

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+#!/usr/bin/env python
+
+# author: Zachary Sexton
+# date: 8-31-21
+
+from pip._internal import main as pipmain
+
+def uninstall(package_name):
+ """
+ Install a python package from within the python SV Interpreter.
+
+ Parameters
+ ----------
+
+ package_name : str
+ python package name for lookup within the site-packages
+ directory for the SV Interpreter
+
+ Returns
+ -------
+
+ success : bool
+ if a package was successfully uninstalled success will be True,
+ otherwise success will return False
+ """
+ # Sanitizing Inputs for package requirements
+ if not isinstance(package_name,str):
+ print('package_name argument must be of type -> str')
+ return False
+ try:
+ pipmain(['uninstall',package_name])
+ success = True
+ except:
+ print('package uninstallation failed')
+ success = False
+ return success