I want to use both the numpy and the pydantic plugins for mypy, I tried the following in the mypy.ini:
[mypy]
plugins = [ numpy.typing.mypy_plugin, pydantic.mypy ]
# ...
It needs to be configured as comma-separated string instead of an actual list, see the docs. This works:
[mypy]
plugins = numpy.typing.mypy_plugin, pydantic.mypy
# ...
Related
I am using Python 3.9.2 with sphinx-build 3.5.2. I have created a project with the following directory and file structure
core_utilities
|_core_utilities
| |_ __init__.py
| |_read_files.py
|_docs
|_ sphinx
|_Makefile
|_conf.pg
|_source
| |_conf.py
| |_index.rst
| |_read_files.rst
|_build
The read_files.py file contains the following code. NOTE: I simplified this example so it would not have distracting information. Within this code their is one class that contains one member function to read a text file, look for a key word and read the variable to the right of the keyword as a numpy.float32 variable. The stand-alone function written to read in a csv file with specific data types and save it to a pandas dataframe.
# Import packages here
import os
import sys
import numpy as np
import pandas as pd
from typing import List
class ReadTextFileKeywords:
def __init__(self, file_name: str):
self.file_name = file_name
if not os.path.isfile(file_name):
sys.exit('{}{}{}'.format('FATAL ERROR: ', file_name, ' does not exist'))
# ----------------------------------------------------------------------------
def read_double(self, key_words: str) -> np.float64:
values = self.read_sentence(key_words)
values = values.split()
return np.float64(values[0])
# ================================================================================
# ================================================================================
def read_csv_columns_by_headers(file_name: str, headers: List[str],
data_type: List[type],
if not os.path.isfile(file_name):
sys.exit('{}{}{}'.format('FATAL ERROR: ', file_name, ' does not exist'))
dat = dict(zip(headers, data_type))
df = pd.read_csv(file_name, usecols=headers, dtype=dat, skiprows=skip)
return df
The conf.py file as the following information in it.
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('../../../core_utilities'))
# -- Project information -----------------------------------------------------
project = 'Core Utilities'
copyright = 'my copyright'
author = 'my name'
# The full version, including alpha/beta/rc tags
release = '0.1.0'
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.todo', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc',
'sphinx.ext.autosummary', 'sphinx.ext.githubpages']
autodoc_member_order = 'groupwise'
autodoc_default_flags = ['members', 'show-inheritance']
autosummary_generate = True
autodock_mock_imports = ['numpy']
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'nature'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
The index.rst file has the following information.
. Core Utilities documentation master file, created by
sphinx-quickstart
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to Core Utilities's documentation!
==========================================
.. toctree::
:maxdepth: 2
:caption: Contents:
read_files
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
and the read_files.rst file has the following information
**********
read_files
**********
The ``read_files`` module contains methods and classes that allow a user to read different
types of files in different ways. Within the module a user will find functionality that
allows them to read text files and csv files by columns and keywords. This module
also contains functions to read sqlite databases, xml files, json files, yaml files,
and html files
.. autoclass:: test.ReadTextFileKeywords
:members:
.. autofunction:: test.read_csv_columns_by_headers
In addition, I am using a virtual environment that is active when I try to compile this with command line. I run the following command to compile html files with sphinx.
sphinx-build -b html source build
When I run the above command it fails with the following error.
WARNING: autodoc: failed to import class 'ReadTextFileKeywords' from module 'read_files'; the following exception was raised; No module named pandas.
If I delete the line from pandas import pd and then delete the function read_csv_columns_by_headers along with the call to the function in the read_files.rst file, everything compiles fine. It appears that for some reason sphinx is able to find numpy, but it for some reason does not seem to recognize pandas, although both exist in the virtual environment and were loaded with a pip3 install statement. Does anyone know why sphinx is able to find other modules, but not pandas?
Add pandas to autodoc
autodoc_mock_imports = ['numpy','pandas']
I am trying to document a Python class using sphinx. I am used Python 3.9.2 and sphinx-build 3.5.2. I am running the command sphinx-build -b html source build to transform the .rst files into .html files. I have already successfully executed this configuration on other classes and functions in the code-suite, so I know their is nothing wrong with the way I have organized my files. When I run the command I get the following error;
Warning: autodoc: failed to import class 'ReadTextFileKeywords' from module 'read_files'; the following exception was raised: No module named pandas
I do have the most recent version of pandas loaded globally and in my virtual environment. Does anyone know why it cannot load pandas and how I can fix this issue?
For reference, the file structure looks like this;
core_utilities
|_core_utilities
|_docs
|_sphinx
|_Makefile
|_build
| |_html files
|_source
|_index.rst
|_Introduction.rst
|_read_files.rst
|_operating_system.rst
|_conf.py
The conf.py file has the following information
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
import os
import sys
sys.path.insert(0, os.path.abspath('../../../core_utilities'))
# -- Project information -----------------------------------------------------
project = 'Core Utilities'
copyright = '2021, Jonathan A. Webb'
author = 'Jonathan A. Webb'
# The full version, including alpha/beta/rc tags
release = '0.1.0'
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = ['sphinx.ext.todo', 'sphinx.ext.viewcode', 'sphinx.ext.autodoc',
'sphinx.ext.autosummary', 'sphinx.ext.githubpages']
autodoc_member_order = 'groupwise'
autodoc_default_flags = ['members', 'show-inheritance']
autosummary_generate = True
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = []
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'nature'
# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ['_static']
and the index file has the following format
.. Core Utilities documentation master file, created by
sphinx-quickstart
You can adapt this file completely to your liking, but it should at least
contain the root `toctree` directive.
Welcome to Core Utilities's documentation!
==========================================
.. toctree::
:maxdepth: 2
:caption: Contents:
Introduction
operating_system
read_files
Indices and tables
==================
* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
Sphinx works just fine when I import docstrings from the operating_system module, so I know that is not the problem. It fails when I try to import from the read_files module. The read_files.rst file has hte following format.
**********
read_files
**********
The ``read_files`` module contains methods and classes that allow a user to read different
types of files in different ways. Within the module a user will find functionality that
allows them to read text files and csv files by columns and keywords. This module
also contains functions to read sqlite databases, xml files, json files, yaml files,
and html files
.. autoclass:: read_files.ReadTextFileKeywords
:members:
And the class it is reading, to include the file has the following format
# Import packages here
import os
import sys
import numpy as np
import pandas as pd
from typing import List
import sqlite3
# ================================================================================
# ================================================================================
# Date: Month Day, Year
# Purpose: Describe the purpose of functions of this file
# Source Code Metadata
__author__ = "Jonathan A. Webb"
__copyright__ = "Copyright 2021, Jon Webb Inc."
__version__ = "1.0"
# ================================================================================
# ================================================================================
# Insert Code here
class ReadTextFileKeywords:
"""
A class to find keywords in a text file and the the variable(s)
to the right of the key word. This class must inherit the
``FileUtilities`` class
:param file_name: The name of the file being read to include the
path-link
For the purposes of demonstrating the use of this class, assume
a text file titled ``test_file.txt`` with the following contents.
.. code-block:: text
sentence: This is a short sentence!
float: 3.1415 # this is a float comment
double: 3.141596235941 # this is a double comment
String: test # this is a string comment
Integer Value: 3 # This is an integer comment
float list: 1.2 3.4 4.5 5.6 6.7
double list: 1.12321 344.3454453 21.434553
integer list: 1 2 3 4 5 6 7
"""
def __init__(self, file_name: str):
self.file_name = file_name
if not os.path.isfile(file_name):
sys.exit('{}{}{}'.format('FATAL ERROR: ', file_name, ' does not exist'))
I am unable to run the feature file. whenever i tried to run the file
i am getting the below stack trace
Exception in thread "main" Usage: java cucumber.api.cli.Main [options] [
[FILE|DIR][:LINE[:LINE]*] ]+
Options:
-g, --glue PATH Where glue code (step definitions and hooks) is loaded from.
-f, --format FORMAT[:PATH_OR_URL] How to format results. Goes to STDOUT unless PATH_OR_URL is specified.
Built-in FORMAT types: junit, html, pretty, progress, json.
FORMAT can also be a fully qualified class name.
-t, --tags TAG_EXPRESSION Only run scenarios tagged with tags matching TAG_EXPRESSION.
-n, --name REGEXP Only run scenarios whose names match REGEXP.
-d, --[no-]-dry-run Skip execution of glue code.
-m, --[no-]-monochrome Don't colour terminal output.
-s, --[no-]-strict Treat undefined and pending steps as errors.
--snippets Snippet name: underscore, camelcase
--dotcucumber PATH_OR_URL Where to write out runtime information. PATH_OR_URL can be a file system
path or a URL.
-v, --version Print version.
-h, --help You're looking at it.
cucumber.runtime.CucumberException: Unknown option: --plugin
at cucumber.runtime.RuntimeOptions.parse(RuntimeOptions.java:119)
at cucumber.runtime.RuntimeOptions.<init>(RuntimeOptions.java:50)
at cucumber.runtime.RuntimeOptions.<init>(RuntimeOptions.java:44)
at cucumber.api.cli.Main.run(Main.java:20)
at cucumber.api.cli.Main.main(Main.java:16)
Please help me to resolve the problem
You normally get this issue if you did not set cucumberOptions correctly on your cukes files.
For example:
#RunWith(Cucumber.class)
#CucumberOptions( dryRun = false, strict = true, features = "src/test/features/com/sample", glue = "com.sample",
tags = { "~#wip", "#executeThis" }, monochrome = true,
format = { "pretty", "html:target/cucumber", "json:target_json/cucumber.json", "junit:taget_junit/cucumber.xml" } )
public class RunCukeTest {
}
Hi I also had this issue as well, and I did the following to resolve it, thanks to the comments of Anusha from video https://youtu.be/pD4B839qfos
-the main trick is to firstly change the jar files you have as follows
cucumber-core-1.2.5.jar
cucumber-java-1.2.5.jar
cucumber-junit-1.2.5.jar
or any of the above, from 1.2.4 upwards
- also update the following selenium-server-standalone-2.42.0.jar and upwards
- also change the format keyword to plugin
Once you make the above changes, this should resolve your problem.
I have a class function that downloads packages using the package method in puppet.
class package {
define install( $dependence=File[$dummy_dependence_file])
{
package { $name:
ensure => "installed",
require => $dependence,
}
}
}
I currently use it in my init.pp like so
# install dependencies
$dependence_list = ['glibc.i686','wget','gcc']
#
# ==Actions
# Install glibc, gcc, wget dependency for running sybase
#
# ==Requires
# * http proxy to be setup to get around jpm proxy
package::install { $dependence_list:
dependence => File[ $http_setup_name ],
}
I would like this method to be more generic. Is it possible instead of using a array of dependencies, which I need to edit the init.pp each time. To use a template and read each dependency from a file? Or any other generic method would do...
An example would be great.
you should be able to simply set the requirement within the package and pass an array to the package too:
$my_packages = ['apache2', 'curl', 'wget']
$my_dependencies = [File['a'], File['b'], User['tester']]
package { $my_packages:
ensure => installed,
require => $my_dependencies,
}
Using this type of package should be sufficient for your needs.
However if you want to read the dependency list from a file you can use the 'template' function. ie.
$my_dependencies = template('modulepath/templates/dependency_list.erb')
Finally you're dependency_list.erb would look like this:
[File['a'], File['b'], User['tester']]
and that's all there really is to it!
For more information you can see http://docs.puppetlabs.com/guides/templating.html
Is there a way to tell scons to use a particular file to setup the default environment? I am using TI DSPs and the compiler is something different than cc; I'd like to have one "environment file" that defines where the compiler is, and what the default flags are, and then be able to use this for several projects.
Any suggestions?
You can use the normal python utilities to read a file or process XML and then import it into your env. If you don't have some external file that you need to import into SCons, then you can simply encode the environment in the scons file. If, for some reason, your environment is defined in a Perl dictionary ( as in my case...) you can either try to use PyPerl or convert the Perl dictionary into YAML and then read the YAML into python. ( I was able to do the later, but not the former).
Let's say you simply have a file that you need to read which has environment variables in the form:
ENV_VAR1 ENV_VAL1
ENV_VAR2 ENV_VAL2
...
You could import this into your SConstruct.py file like:
import os
env_file = open('PATH_TO_ENV_FILE','r')
lines = env.file.readlines()
split_regex = re.compile('^(?P<env_var>[\w_]+) *(?P<env_val>.*)')
for line in lines:
regex_search = split_regex.search(line)
if regex_search:
env_var = regex_search.group('env_var')
env_val = regex_search.group('env_val').strip()
os.environ[env_var] = env_val
base_env = Environment(ENV=os.environ)
# even though the below lines seem redundant, it was necessary in my build
# flow...
for key in os.environ.iterkeys():
base_env[key] = os.environ[key]
If you want to stick this ugliness inside a different file and then import it from your main SConstruct.py file, you can add the following to enable access to the 'Environment' class from your other file:
from SCons.Environment import *
Then in your main SConstruct.py file, import the env file like:
from env_loader import *
SInclusion file:
...
myenv = Environment(...)
...
SConstruct file:
...
execfile('SInclusion')
...
myenv.Object(...)
...