I have a migrations folder in my app:
$ ls src/migrations/
README __pycache__ alembic.ini env.py script.py.mako versions
And a mypy config file:
$ cat setup.cfg
[mypy]
ignore_missing_imports = True
disallow_untyped_calls = True
disallow_incomplete_defs = True
[mypy-*.migrations.*]
ignore_errors = True
But when I run
mypy src
I still see errors from the migrations folder:
src/migrations/env.py:95: error: Call to untyped function "run_migrations_offline" in typed context
src/migrations/env.py:97: error: Call to untyped function "run_migrations_online" in typed context
why is that and how to fix this?
My version is:
$ mypy --version
mypy 0.812
Related
I'm quite new to Nix and I'm trying to create a very simple shell.nix script file.
Unfortunately I need an old package: mariadb-10.4.21. After reading and searching a bit I found out that version 10.4.17 (would've been nice to have the exact version but I couldn't find it) is in channel nixos-20.09, but when I do
$ nix-shell --version
nix-shell (Nix) 2.5.1
$ cat shell.nix
let
pkgs = import <nixpkgs> {};
# git ls-remote https://github.com/nixos/nixpkgs nixos-20.09
pkgs-20_09 = import (builtins.fetchGit {
name = "nixpks-20.09";
url = "https://github.com/nixos/nixpkgs";
ref = "refs/heads/nixos-20.09";
rev = "1c1f5649bb9c1b0d98637c8c365228f57126f361";
}) {};
in
pkgs.stdenv.mkDerivation {
pname = "test";
version = "0.1.0";
buildInputs = [
pkgs-20_09.mariadb
];
}
$ nix-shell
it just waits indefinitely without doing anything. But if I do
$ nix-shell -p mariadb -I nixpkgs=https://github.com/NixOS/nixpkgs/archive/1c1f5649bb9c1b0d98637c8c365228f57126f361.tar.gz
[...]
/nix/store/yias2v8pm9pvfk79m65wdpcby4kiy91l-mariadb-server-10.4.17
[...]
copying path '/nix/store/yias2v8pm9pvfk79m65wdpcby4kiy91l-mariadb-server-10.4.17' from 'https://cache.nixos.org'...
[nix-shell:~/Playground]$ mariadb --version
mariadb Ver 15.1 Distrib 10.4.17-MariaDB, for Linux (x86_64) using readline 5.1
it works perfectly.
What am I doing wrong in the script for it to halt?
EDIT: I got a bit more info by running
$ nix-shell -vvv
[...]
did not find cache entry for '{"name":"nixpks-20.09","rev":"1c1f5649bb9c1b0d98637c8c365228f57126f361","type":"git"}'
did not find cache entry for '{"name":"nixpks-20.09","ref":"refs/heads/nixos-20.09","type":"git","url":"https://github.com/nixos/nixpkgs"}'
locking path '/home/test/.cache/nix/gitv3/17blyky0ja542rww32nj04jys1r9vnkg6gcfbj83drca9a862hwp.lock'
lock acquired on '/home/test/.cache/nix/gitv3/17blyky0ja542rww32nj04jys1r9vnkg6gcfbj83drca9a862hwp.lock.lock'
fetching Git repository 'https://github.com/nixos/nixpkgs'...
Is it me or it seems like it's trying to fetch from two different sources? As far as I understood all three url, rev and ref are needed for git-fetching, but it looks like if it's splitting them.
EDIT2: I've been trying with fetchFromGitHub
pkgs-20_09 = import (pkgs.fetchFromGitHub {
name = "nixpks-20.09";
owner = "nixos";
repo = "nixpkgs";
rev = "1c1f5649bb9c1b0d98637c8c365228f57126f361";
sha256 = "0f2nvdijyxfgl5kwyb4465pppd5vkhqxddx6v40k2s0z9jfhj0xl";
}) {};
and fetchTarball
pkgs-20_09 = import (builtins.fetchTarball "https://github.com/NixOS/nixpkgs/archive/1c1f5649bb9c1b0d98637c8c365228f57126f361.tar.gz") {};
and both work just fine. I'll use fetchFromGitHub from now on but it'd be interesting to now why fetchGit doesn't work.
I'm building my .NET Core app in Travis CI using Cake script, when it comes to
var d = new DirectoryInfo(packageOutputPath.ToString());
var Files = d.GetFiles("*.nupkg").Select(x => new FilePath(x.FullName));
var key = EnvironmentVariable("NugetKey");
NuGetPush(Files, new NuGetPushSettings {
Source = Variables.NugetSource,
ApiKey = key
command I get:
An error occurred when executing task 'PushPackage'.
Error: One or more errors occurred. (Permission denied)
Permission denied
My .travis.yml file:
sudo: required
language: csharp
mono: none
dotnet: 2.1.402
before_install:
- chmod +x build.sh
script:
- ./build.sh --Target="PushPackage"
I have tried replacing - ./build.sh --Target="PushPackage" with - sudo bash build.sh --Target="PushPackage" but this did not help. Any suggestions why I'm getting this error?
build.sh file was builded according to this. Whole repo is here.
You should be using the DotNetCoreNuGetPush alias when using the .NET CLI, NuGetPush requires nuget.exe.
Example:
DirectoryPath packageOutputPath = MakeAbsolute(Directory("./nuget/"));
var settings = new DotNetCoreNuGetPushSettings
{
Source = "https://www.example.com/nugetfeed",
ApiKey = "4003d786-cc37-4004-bfdf-c4f3e8ef9b3a"
};
foreach(var file in GetFiles($"{packageOutputPath}/*.nupkg"))
{
DotNetCoreNuGetPush(file.FullPath, settings);
}
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 install hugo-academic theme in blogdown. Within my site directory I ran R and installed with
blogdown::install_theme("gcushen/hugo-academic")
After installing I edited the config.toml file as shown below:
baseurl = "/"
relativeurls = true
languageCode = "en-us"
title = "A Hugo website"
theme = "hugo-academic"
googleAnalytics = ""
disqusShortname = ""
ignoreFiles = ["\\.Rmd$", "_files$", "_cache$"]
After that when I try to serve site with
blogdown::serve_site(),
I get the following error:
Started building sites ...
ERROR 2017/06/01 20:02:50 Error while rendering "page": template: theme/_default/single.html:10:7: executing "theme/_default/single.html" at <partial "article_met...>: error calling partial: template: theme/partials/article_metadata.html:7:24: executing "theme/partials/article_metadata.html" at <$.Site.Params.date_f...>: invalid value; expected string
Started building sites ...
ERROR 2017/06/01 20:02:50 Error while rendering "page": template: theme/_default/single.html:10:7: executing "theme/_default/single.html" at <partial "article_met...>: error calling partial: template: theme/partials/article_metadata.html:7:24: executing "theme/partials/article_metadata.html" at <$.Site.Params.date_f...>: invalid value; expected string
The system cannot find the path specified.
Error in shell(cmd, mustWork = TRUE, intern = intern) :
'"C:\Users\Suman\AppData\Roaming\Hugo\hugo.exe" -b / -D -F -d "public" -t hugo-academic' execution failed with error code 1
In addition: Warning messages:
1: running command '"C:\Users\Suman\AppData\Roaming\Hugo\hugo.exe" -b / -D -F -d "public" -t hugo-academic' had status 65535
2: running command '"C:\Users\Suman\AppData\Roaming\Hugo\hugo.exe" -b / -D -F -d "public" -t hugo-academic' had status 65535
3: running command 'C:\WINDOWS\system32\cmd.exe /c "C:\Users\Suman\AppData\Roaming\Hugo\hugo.exe" -b / -D -F -d "public" -t hugo-academic' had status 1
Any help to solve this?
Note: I am on Windows 10 64 bit OS.
Judging from the error message, you need to add a date_format parameter to your config.toml file. Try adding this at the end:
[params]
date_format = "Mon, Jan 2, 2006"
Take a look at the example config file for more settings that you can change.
I am learning Grunt and want to use load-grunt-config to start with. Here is my code :
Gruntfile.js
module.exports = function (grunt){
var path = require('path');
require('load-grunt-config')(grunt, {
configPath: path.join(process.cwd(), 'grunt-tasks'),
});
grunt.registerTask('install',['test']);
};
I have grunt-tasks folder in root directory of my project along with Gruntfile.js and in that I have included test.js
test.js
module.exports = {
test :{
local : {
}
}
};
Now when I say grunt install from command line and using CWD as my project's root directory I get following error :
Warning: Task "test" not found. Use --force to continue.
and when I include following segment in Gruntfile.js
loadGruntTasks : {
pattern : '*'
}
I get following error :
>> Local Npm module "load-grunt-config" not found. Is it installed?
Warning: Task "test" not found. Use --force to continue.
May I know what I don't understand here?