merge fresh main

.github/workflows/docs.yml

@@ -18,7 +18,6 @@ jobs:
         run: sudo apt-get install build-essential libpoppler-cpp-dev pkg-config python3-dev -y
       - name: Install sec-certs and deps
         run: |
-          pip install -r requirements/requirements.txt
           pip install -r requirements/dev_requirements.txt
           pip install -e .
       - name: Build docs

.github/workflows/pre-commit.yml

@@ -0,0 +1,18 @@
+name: Lint (Ruff, MyPy)
+on:
+  push:
+  workflow_dispatch:
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.8"
+      - name: Install dependencies
+        run: |
+          sudo apt-get install build-essential libpoppler-cpp-dev pkg-config python3-dev -y
+          pip install -r requirements/dev_requirements.txt
+      - name: Run pre-commit
+        run: pre-commit run --all-files

.github/workflows/tests.yml

@@ -18,11 +18,9 @@ jobs:
           python-version: "3.8"
           cache: "pip"
           cache-dependency-path: |
-            requirements/requirements.txt
             requirements/test_requirements.txt
       - name: Install python dependencies
         run: |
-          pip install -r requirements/requirements.txt
           pip install -r requirements/test_requirements.txt
       - name: Install sec-certs
         run: |

.pre-commit-config.yaml

@@ -1,16 +1,12 @@
 repos:
-  - repo: https://github.com/psf/black
-    rev: 23.1.0
-    hooks:
-      - id: black
-        args: ["--check", "--target-version", "py38"]
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
-    # Ruff version.
-    rev: "v0.0.239"
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.1.5
     hooks:
       - id: ruff
+      - id: ruff-format
+        args: ["--check"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.3.0"
+    rev: "v1.6.1"
     hooks:
       - id: mypy
         additional_dependencies:

CONTRIBUTING.md

@@ -18,6 +18,7 @@ Requirements are maintained with [pip-tools](https://github.com/jazzband/pip-too
 - List actual dependencies in [pyproject.toml](https://github.com/crocs-muni/sec-certs/blob/main/pyproject.toml) without pinning them.
 - Additionally, [compile.sh](https://github.com/crocs-muni/sec-certs/blob/main/requirements/compile.sh) script is used to compile pinned versions of requirements that reside in `.txt` files in the same folder.
 - Tests, linting and Docker all run against this reproducible environment of pinned requirements.
+- To install all requirements, use `pip install -U pip-tools && pip-sync requirements/all_requirements.txt`
 
 ## Branches
 
@@ -43,9 +44,7 @@ Note on single-sourcing the package version: More can be read [here](https://pac
 All commits shall pass the lint pipeline of the following tools:
 
 - Mypy (see [pyproject.toml](https://github.com/crocs-muni/sec-certs/blob/main/pyproject.toml) for settings)
-- Black (see [pyproject.toml](https://github.com/crocs-muni/sec-certs/blob/main/pyproject.toml) for settings)
 - Ruff (see [pyproject.toml](https://github.com/crocs-muni/sec-certs/blob/main/pyproject.toml) for settings)
-- PyUpgrade
 
 These tools can be installed via [dev_requirements.txt](https://github.com/crocs-muni/sec-certs/blob/main/dev_requirements.txt) You can use [pre-commit](https://pre-commit.com/) tool to register git hook that will evalute these checks prior to any commit and abort the commit for you. Note that the pre-commit is not meant to automatically fix the issues, just warn you.
 
@@ -59,12 +58,12 @@ pre-commit run --all-files
 
 To ivoke the tools manually, you can, in the repository root, use:
 - Mypy: `mypy .`
-- Black: `black --check .` (without the flag to reformat)
 - Ruff: `ruff ." (or with `--fix` flag to apply fixes)
+- Ruff formatL `ruff format --check .`
 
 ## Documentation
 
 Every public method of a module that can be leveraged as an API by user should be documented. The docstrng style should
 be `sphinx-oneline`.
 
-The documentation is built using `sphinx` with `mnyst` extension that allows for markdown files. Folder `notebooks/examples` is symbolically linked to `/docs` and its contents will be automatically parsed. These notebooks are supposed to be runnable from Binder.
+The documentation is built using `sphinx` with `mnyst` extension that allows for markdown files. Folder `notebooks/examples` is symbolically linked to `/docs` and its contents will be automatically parsed. These notebooks are supposed to be runnable from Binder.

Dockerfile

@@ -56,15 +56,14 @@ ENV PATH="${VENV_PATH}/bin:$PATH"
 
 # Install dependencies, notebook is because of mybinder.org
 RUN \
-  pip3 install -U pip && \
-  pip3 install wheel && \
-  pip3 install -r requirements/requirements.txt && \
+  pip3 install -U pip wheel pip-tools && \
+  pip-sync requirements/all_requirements.txt && \
   pip3 install --no-cache notebook jupyterlab && \
   pip3 install -e . && \
   python3 -m spacy download en_core_web_sm
 
 # just to be sure that pdftotext is in $PATH
 ENV PATH /usr/bin/pdftotext:${PATH}
 
-# # Run the application:
-# CMD ["python3", "./cc_cli.py"]
+# Run the application:
+ENTRYPOINT ["sec-certs"]

README.md

@@ -2,7 +2,9 @@
 
 ![](docs/_static/logo.png)
 
-A tool for data scraping and analysis of security certificates from Common Criteria and FIPS 140-2/3 frameworks. This project is developed by the [Centre for Research On Cryptography and Security](https://crocs.fi.muni.cz) at Masaryk University, Czech Republic.
+A tool for data scraping and analysis of security certificates from Common Criteria and FIPS 140-2/3 frameworks.
+
+<!-- This project is developed by the [Centre for Research On Cryptography and Security](https://crocs.fi.muni.cz) at Masaryk University, Czech Republic. -->
 
 [![Website](https://img.shields.io/website?down_color=red&down_message=offline&style=flat-square&up_color=SpringGreen&up_message=online&url=https%3A%2F%2Fseccerts.org)](https://seccerts.org)
 [![Website](https://img.shields.io/website?label=docs&down_color=red&down_message=offline&style=flat-square&up_color=SpringGreen&up_message=online&url=https%3A%2F%2Fseccerts.org/docs/index.html)](https://seccerts.org/docs/index.html)
@@ -58,8 +60,8 @@ df_2015_and_newer = df.loc[df.year_from > 2014]
 df.year_from.value_counts().sort_index().plot.line()
 ```
 
-## Authors
+<!-- ## Authors
 
 This work is being done at [CRoCS MUNI](https://crocs.fi.muni.cz/) by Adam Janovsky, Jan Jancar, Petr Svenda, Jiri Michalik, Lukasz Chmielewski and other contributors. This work was supported by the Internal grant agency of Masaryk University, CZ.02.2.69/0.0/0.0/19_073/0016943.
 
-![](docs/_static/logolink_OP_VVV_hor_barva_eng.jpg)
+![](docs/_static/logolink_OP_VVV_hor_barva_eng.jpg) -->

docs/conf.py

@@ -18,7 +18,8 @@
 # -- Project information -----------------------------------------------------
 
 project = "sec-certs"
-copyright = "CRoCS MUNI | 2020-2023"
+copyright = "Anonymized | 2020-2023"
+# copyright = "CRoCS MUNI | 2020-2023"
 
 # Note thas this inference won't work from Docker: https://github.com/pypa/setuptools_scm/#usage-from-docker
 release = ".".join(get_version("sec-certs").split(".")[:3])

docs/index.md

@@ -21,8 +21,7 @@ Each of the notebooks can be launched interactively in MyBinder by clicking on 
 :maxdepth: 1
 Seccerts homepage <https://seccerts.org/>
 Seccerts docs <https://seccerts.org/docs>
-GitHub repo <https://github.com/crocs-muni/sec-certs>
-Seccerts PyPi <https://pypi.org/project/sec-certs/>
+GitHub repo <https://anonymous.4open.science/r/sec-certs-7A92>
 ```
 
 ```{toctree}