From c5b27a3ecdf4799f4f9dee628f9a2b867ca90a8c Mon Sep 17 00:00:00 2001
From: Remi PLANEL <rplanel@pasteur.fr>
Date: Thu, 23 Nov 2023 13:26:57 +0100
Subject: [PATCH] Front matter linter
---
.gitlab-ci.yml | 41 +++++++++++--------
.../df-wiki-cli/df_wiki_cli/content/main.py | 6 ++-
2 files changed, 27 insertions(+), 20 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c44a22fd..1bc41c11 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,6 +4,11 @@ workflow:
when: never
- when: always
+
+
+
+
+
# Functions that should be executed before the build script is run
variables:
@@ -15,6 +20,8 @@ variables:
# prod
HOST_PROD: 'defense-finder.pasteur.cloud'
MEILI_HOST_PROD: 'defense-finder-meilisearch.pasteur.cloud'
+ PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
+
cache:
@@ -44,9 +51,17 @@ stages:
# Build df-wiki-cli package
+.df-wiki-cli-run:
+ image: python:3.11-bullseye
+ cache: # Pip's cache doesn't store the python packages
+ paths: # https://pip.pypa.io/en/stable/topics/caching/
+ - .cache/pip
+ before_script:
+ - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
+
build:df-wiki-cli:
- stage: build-df-cli
image: python:3.11-bullseye
+ stage: build-df-cli
before_script:
- cd packages/df-wiki-cli/
- pip install poetry
@@ -165,13 +180,11 @@ delete-meili-helm-release:prod:
# lint
lint:
- image: python:3.11-bullseye
+ extends: .df-wiki-cli-run
stage: lint
- before_script:
- - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
- - cd content/3.defense-systems
script:
- - find . -name '*.md' -print0 | xargs -0 -I {} df-wiki-cli content lint --file {}
+ - cd content/3.defense-systems
+ - find . -name '*.md' ! -name '0.index.md' -print0 | xargs -0 -I {} df-wiki-cli content lint --file {}
when: manual
rules:
- if: $CI_COMMIT_BRANCH != "main"
@@ -179,12 +192,10 @@ lint:
# Update Meili search indexes
.update-meilisearch-index:
+ extends: .df-wiki-cli-run
stage: update-meilisearch-indexes
- image: python:3.11-bullseye
variables:
MEILI_HOST: "http://localhost:7700"
- before_script:
- - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
script:
- >
df-wiki-cli
@@ -225,12 +236,10 @@ update-meilisearch-index:prod:
############# get-meili-key ###############
.set-meili-env:
- image: python:3.11-bullseye
+ extends: .df-wiki-cli-run
stage: get-meili-key
variables:
MEILI_HOST: "http://localhost:7700"
- before_script:
- - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
script:
- >
df-wiki-cli
@@ -262,10 +271,8 @@ set-meili-env:prod:
##############################
get-zotero:
- image: python:3.11-bullseye
+ extends: .df-wiki-cli-run
stage: get-data
- before_script:
- - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
script:
- df-wiki-cli articles --key ${ZOTERO_API_KEY} --output public/articles.json
artifacts:
@@ -275,10 +282,8 @@ get-zotero:
- if: $CI_COMMIT_BRANCH == "main"
get-pfam:
- image: python:3.11-bullseye
+ extends: .df-wiki-cli-run
stage: get-data
- before_script:
- - pip install df-wiki-cli --index-url https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.pasteur.fr/api/v4/projects/5222/packages/pypi/simple
script:
- df-wiki-cli pfam --output public/pfam-a-hmm.csv
artifacts:
diff --git a/packages/df-wiki-cli/df_wiki_cli/content/main.py b/packages/df-wiki-cli/df_wiki_cli/content/main.py
index 11113150..b869c668 100644
--- a/packages/df-wiki-cli/df_wiki_cli/content/main.py
+++ b/packages/df-wiki-cli/df_wiki_cli/content/main.py
@@ -1,9 +1,9 @@
import typer
+import sys
from typing_extensions import Annotated
from typing import Optional, List
from pathlib import Path
from pydantic import BaseModel, ValidationError
-from pydantic_yaml import parse_yaml_raw_as, to_yaml_str
import frontmatter
from enum import Enum
from rich.console import Console
@@ -70,7 +70,9 @@ def lint(
# pprint(exc.errors(), expand_all=True)
for err in exc.errors():
console.print(
- f"[red]{err['msg']} : {err['type']} {' -> '.join(err['loc'])}"
+ f"[red]{err['msg']} : {err['type']} {' -> '.join([str(l) for l in err['loc']])}"
)
+ # raise
+ sys.exit(1)
else:
console.print("[green] Everything is alright")
--
GitLab