I've been trying to configure my pre-commit config file to ignore similiarities on imports and docstrings as described in: https://pylint.pycqa.org/en/latest/technical_reference/features.html?highlight=similar#similarities-checker-options
But I don't use any of .pylintrc files, just the .pre-commit-config.yaml.
Below is a snippet from .pre-commit-config.yaml
- id: pylint
name: pylint
entry: pylint
language: python
require_serial: true
types_or: [python, pyi]
exclude: 'kedro-init'
args: ['--disable=E0401,E1101,E1102,R0913,R0914,W0703,E0602,C0103,C0114,
W0102,C0330,C0326,W0107,R1716,R0902,E0611,E1124', '--fail-under=7.5',
'--ignore-imports=yes', '--ignore-docstrings=yes'] #this last line does not work
Is there any way to specify those options on the args key?
Thx!
python version: 3.8.x
pylint version: 2.12.3
If you retype your args in .pre-commit-config.yaml as below, it should work.
- repo: local
hooks:
- id: pylint
name: pylint
entry: pylint
language: python
require_serial: true
types_or: [python, pyi]
exclude: 'kedro-init'
args: ["--ignore=E0401,E1101,E1102,R0913,R0914,W0703,E0602,C0103,
C0114, W0102,C0330,C0326,W0107,R1716,R0902,E0611,E1124",
"--fail-under=7.5"]
Related
I have the following .pre-commit-config.yaml file. At the first line, I have this top level exclude path to exclude all checks in that folder, but for some reason, the mypy hook still outputs errors from files in that folder. Could someone help me understand what's going on? Thanks.
exclude: "src/project/proto/"
default_language_version:
python: python3.8
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v4.4.0
hooks:
- id: check-ast
- id: check-docstring-first
- id: check-executables-have-shebangs
- id: check-json
- id: check-merge-conflict
- id: check-yaml
- id: debug-statements
- id: end-of-file-fixer
- id: trailing-whitespace
- repo: https://github.com/asottile/pyupgrade
rev: v3.2.2
hooks:
- id: pyupgrade
- repo: https://github.com/asottile/reorder_python_imports
rev: v3.9.0
hooks:
- id: reorder-python-imports
args: [--py3-plus]
- repo: https://github.com/asottile/add-trailing-comma
rev: v2.3.0
hooks:
- id: add-trailing-comma
- repo: https://github.com/pre-commit/mirrors-mypy
rev: v0.991
hooks:
- id: mypy
args: [--strict]
additional_dependencies:
[types-protobuf>=4.21.0.0, types-termcolor>=1.1.6, pytest>=7.2.0]
- repo: https://github.com/PyCQA/flake8
rev: 6.0.0
hooks:
- id: flake8
I also have this mypy.ini. Just in case, I missed anything here.
[mypy]
python_version = 3.8
mypy_path = ./src:./tests
[mypy-lark.*]
ignore_missing_imports = True
it is working, but not in the way you expect
mypy performs dynamic analysis and will follow imports. pre-commit is not passing those filenames onto mypy but they are being checked due to follow-imports
you will need to also use mypy's settings to ignore errors there
disclaimer: I created pre-commit
I'm trying to learn how to use script plugin. I'm following script plugin docs here but not able to make it work.
I've tried to use the plugin in two ways. The first, when cloudify.interface.lifecycle.start operation is mapped directly to a script:
tosca_definitions_version: cloudify_dsl_1_3
imports:
- 'http://www.getcloudify.org/spec/cloudify/4.5.5/types.yaml'
node_templates:
Import_Project:
type: cloudify.nodes.WebServer
capabilities:
scalable:
properties:
default_instances: 1
interfaces:
cloudify.interfaces.lifecycle:
start:
implementation: scripts/create_project.sh
inputs: {}
The second with a direct mapping:
tosca_definitions_version: cloudify_dsl_1_3
imports:
- 'http://www.getcloudify.org/spec/cloudify/4.5.5/types.yaml'
node_templates:
Import_Project:
type: cloudify.nodes.WebServer
capabilities:
scalable:
properties:
default_instances: 1
interfaces:
cloudify.interfaces.lifecycle:
start:
implementation: script.script_runner.tasks.run
inputs:
script_path: scripts/create_project.sh
I've created a directory named scripts and placed the below create_project.sh script in this directory:
#! /bin/bash -e
ctx logger info "Hello to this world"
hostname
I'm getting errors while validating the blueprint.
Error when operation is mapped directly to a script:
[2019-04-13 13:29:40.594] [DEBUG] DslParserExecClient - got output from dsl parser Could not extract plugin from operation mapping 'scripts/create_project.sh', which is declared for operation 'start'. In interface 'cloudify.interfaces.lifecycle' in node 'Import_Project' of type 'cloudify.nodes.WebServer'
in: /opt/cloudify-composer/backend/dev/workspace/2/tmp-27O0e1t813N6as
in line: 3, column: 2
path: node_templates.Import_Project
value: {'interfaces': {'cloudify.interfaces.lifecycle': {'start': {'implementation': 'scripts/create_project.sh', 'inputs': {}}}}, 'type': 'cloudify.nodes.WebServer', 'capabilities': {'scalable': {'properties': {'default_instances': 1}}}}
Error when using a direct mapping:
[2019-04-13 13:25:21.015] [DEBUG] DslParserExecClient - got output from dsl parser node 'Import_Project' has no relationship which makes it contained within a host and it has a plugin 'script' with 'host_agent' as an executor. These types of plugins must be installed on a host
in: /opt/cloudify-composer/backend/dev/workspace/2/tmp-279QCz2CV3Y81L
in line: 2, column: 0
path: node_templates
value: {'Import_Project': {'interfaces': {'cloudify.interfaces.lifecycle': {'start': {'implementation': 'script.script_runner.tasks.run', 'inputs': {'script_path': 'scripts/create_project.sh'}}}}, 'type': 'cloudify.nodes.WebServer', 'capabilities': {'scalable': {'properties': {'default_instances': 1}}}}}
What is missing to make this work?
I also found the Cloudify Script Plugin examples from their documentation do not work: https://docs.cloudify.co/4.6/working_with/official_plugins/configuration/script/
However, I found I can make the examples work by adding an executor line in parallel with the implementation line to override the host_agent executor as follows:
tosca_definitions_version: cloudify_dsl_1_3
imports:
- 'http://www.getcloudify.org/spec/cloudify/4.5.5/types.yaml'
node_templates:
Import_Project:
type: cloudify.nodes.WebServer
capabilities:
scalable:
properties:
default_instances: 1
interfaces:
cloudify.interfaces.lifecycle:
start:
implementation: scripts/create_project.sh
executor: central_deployment_agent
inputs: {}
I have written the CWL code which runs the Rscript command in the docker container. I have two files of cwl and yaml and run them by the command:
cwltool --debug a_code.cwl a_input.yaml
I get the output which said that the process status is success but there is no output file and in the result "output": null is reported. I want to know if there is a method to find that the Rscript file has run on the docker successfully. I want actually know about the reason that the output files are null.
The final part of the result is:
[job a_code.cwl] {
"output": null,
"errorFile": null
}
[job a_code.cwl] Removing input staging directory /tmp/tmpUbyb7k
[job a_code.cwl] Removing input staging directory /tmp/tmpUbyb7k
[job a_code.cwl] Removing temporary directory /tmp/tmpkUIOnw
[job a_code.cwl] Removing temporary directory /tmp/tmpkUIOnw
Removing intermediate output directory /tmp/tmpCG9Xs1
Removing intermediate output directory /tmp/tmpCG9Xs1
{
"output": null,
"errorFile": null
}
Final process status is success
Final process status is success
R code:
library(cummeRbund)
cuff<-readCufflinks( dbFile = "cuffData.db", gtfFile = NULL, runInfoFile = "run.info", repTableFile = "read_groups.info", geneFPKM = "genes.fpkm_trac .... )
#setwd("/scripts")
sink("cuff.txt")
print(cuff)
sink()
My cwl file code is:
class: CommandLineTool
cwlVersion: v1.0
id: cummerbund
baseCommand:
- Rscript
inputs:
- id: Rfile
type: File?
inputBinding:
position: 0
- id: cuffdiffout
type: 'File[]?'
inputBinding:
position: 1
- id: errorout
type: File?
inputBinding:
position: 99
prefix: 2>
valueFrom: |
error.txt
outputs:
- id: output
type: File?
outputBinding:
glob: cuff.txt
- id: errorFile
type: File?
outputBinding:
glob: error.txt
label: cummerbund
requirements:
- class: DockerRequirement
dockerPull: cummerbund_0
my input file (yaml file) is:
inputs:
Rfile:
basename: run_cummeR.R
class: File
nameext: .R
nameroot: run_cummeR
path: run_cummeR.R
cuffdiffout:
- class: File
path: cuffData.db
- class: File
path: genes.fpkm_tracking
- class: File
path: read_groups.info
- class: File
path: genes.count_tracking
- class: File
path: genes.read_group_tracking
- class: File
path: isoforms.fpkm_tracking
- class: File
path: isoforms.read_group_tracking
- class: File
path: isoforms.count_tracking
- class: File
path: isoform_exp.diff
- class: File
path: gene_exp.diff
errorout:
- class: File
path: error.txt
Also, this is my Dockerfile for creating image:
FROM r-base
COPY . /scripts
RUN apt-get update
RUN apt-get install -y \
libcurl4-openssl-dev\
libssl-dev\
libmariadb-client-lgpl-dev\
libmariadbclient-dev\
libxml2-dev\
r-cran-plyr\
r-cran-reshape2
WORKDIR /scripts
RUN Rscript /scripts/build.R
ENTRYPOINT /bin/bash
I got the answer!
There were some problems in my program.
1. The docker was not pulled correctly then the cwl couldn't produce any output.
2. The inputs and outputs were not defined mandatory. So I got the success status in the case which I did not have proper inputs and output.
I am trying to create a requirejs optimization config with grunt and almond. Here's the config:
requirejs:
build:
options:
almond: true
dir: 'build'
appDir: ''
baseUrl: '../client'
wrap: true
include: '../client/main'
keepBuildDir: true
paths:
underscore: 'client/vendor/underscore'
jquery : 'client/vendor/jquery'
backbone : 'client/vendor/backbone'
Folder Structure:
Error:
C:\Users\User\Documents\Source\Project>grunt requirejs
Running "requirejs:build" (requirejs) task
>> Error: ENOENT, no such file or directory
>> 'C:\Users\User\Documents\Source\Project\build\models\MenuItem.js'
>> In module tree:
>> ../client/main
Warning: RequireJS failed. Use --force to continue.
Main.js code (written in coffeescript)
requirejs.config(
baseUrl: "client"
shim:
'backbone':
deps: ['jquery']
exports: 'Backbone'
'jquery':
exports: '$'
'underscore':
exports: '_'
paths:
jquery: 'vendor/jquery-1.11.0'
underscore: 'vendor/underscore'
backbone: 'vendor/backbone'
)
define 'start', ()->
window.types =
Models: {}
Collections: {}
Views: {}
null
require ['models/MenuItem', 'views/MenuItem'], (MenuItemModel, MenuItemView)->
view = new MenuItemView(
new MenuItemModel(),
"#app",
'first'
)
view.render();
null
I want to compile my entire project spread across multiple js files into a single file in a way that requirejs would not be needed. I am trying to do this using almond js but the build task does not look for referenced files relative to the path of referring file. Please help me with the correct configuration.
I'm using KnpSnappyBundle for my Symfony project and I'm trying to define some options in my config file. However if I set, for example:
knp_snappy:
pdf:
enabled: true
binary: /usr/local/bin/wkhtmltopdf
options: [ 'no-outline' ]
I get an error:
The option '0' does not exist.
How do I define options for the bundle?
Well, that was kinda dumb of me. YAML to the answer:
knp_snappy:
pdf:
enabled: true
binary: /usr/local/bin/wkhtmltopdf
options:
no-outline: true
The answer is:
knp_snappy:
pdf:
enabled: true
binary: /path/to/wkhtmltopdf
options:
- { name: 'page-size', value: 'A4' }