Lint

.coveragerc

@@ -1,2 +1,2 @@
 [run]
-omit = *HardwareRepository/*
+omit = *HardwareRepository/*

.flake8

@@ -0,0 +1,12 @@
+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 88
+max-complexity = 18
+select = B,C,E,F,W,T4,B9
+exclude =
+    .git,
+    __pycache__,
+    docs/conf.py,
+    build,
+    dist,
+    test,

.github/workflows/build_and_test.yml

@@ -1,4 +1,4 @@
-name: Build and test
+name: Lint and test
 
 on: [push, pull_request]
 
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: ["3.10"] #, "3.9", "3.10"]
+         python-version: ["3.10"] #, "3.9", "3.10"]
 
     # Skip `pull_request` runs on local PRs for which `push` runs are already triggered
     if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
@@ -35,26 +35,23 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: ${{ matrix.python-version }}
-    - name: Add conda to system path
-      run: |
-        # $CONDA is an environment variable pointing to the root of the miniconda directory
-        echo $CONDA/bin >> $GITHUB_PATH
-    - name: Install ldap dependencies
+
+    - name: Install LDAP dependencies
       run: sudo apt-get -y install libsasl2-dev libldap2-dev libssl-dev
-    - name: Install dependencies
-      run: |
-        conda install -c conda-forge mamba
-        mamba env update --file conda-environment.yml --name base
-        pip install -e .
-    - name: Lint with flake8
-      run: |
-        #conda install flake8
-        # stop the build if there are Python syntax errors or undefined names
-        #flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        #flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+    - name: Set up Conda environment
+      uses: mamba-org/setup-micromamba@v1
+      with:
+        micromamba-version: "latest"
+        environment-file: conda-environment.yml
+        cache-environment: true
+        post-cleanup: "all"
+
+    - name: Install MXCuBE
+      run: "${MAMBA_EXE} run --name mxcubeweb poetry install"
+
+    - name: Linting & Code Quality
+      run: "${MAMBA_EXE} run --name mxcubeweb poetry run pre-commit run --all-files"
+
     - name: Test with pytest
-      run: |
-        conda install pytest
-        conda install pytest-cov
-        pytest
+      run: "${MAMBA_EXE} run --name mxcubeweb poetry run pytest"

.pre-commit-config.yaml

@@ -0,0 +1,57 @@
+default_language_version:
+  python: python3.10
+repos:
+  - repo: https://github.com/python-poetry/poetry
+    rev: 1.5.0
+    hooks:
+      - id: poetry-check
+        language_version: python3.10
+  #    - id: poetry-lock
+  #      language_version: python3.10
+  - repo: https://github.com/myint/autoflake
+    rev: v1.6.0
+    hooks:
+      - id: autoflake
+        name: Autoflake
+        args:
+          - --expand-star-imports
+          - --ignore-init-module-imports
+          - --in-place
+          - --remove-duplicate-keys
+          - --ignore-pass-after-docstring
+  - repo: https://github.com/psf/black
+    rev: 22.8.0
+    hooks:
+    - id: black
+      name: Black
+      language_version: python3.10
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-case-conflict
+      - id: check-merge-conflict
+        # exclude files where underlines are not distinguishable from merge conflicts
+        exclude: /README\.rst$|^docs/.*\.rst$
+      - id: check-symlinks
+      - id: check-xml
+      - id: check-yaml
+        exclude: ^.drone\.yml|meta.yaml
+      - id: mixed-line-ending
+        args: ["--fix=lf"]
+  # - repo: https://github.com/PyCQA/isort
+  #   rev: 5.10.1
+  #   hooks:
+  #     - id: isort
+  #       name: Import Sort
+  #       args:
+  #         - --settings=.
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+    - id: flake8
+      name: Flake8
+# Not using bugbear for now
+#      additional_dependencies: ["flake8-bugbear==22.9.11"]
+      exclude: (ui/|test/)

CONTRIBUTING.md

@@ -23,7 +23,7 @@ Pull requests (PR's) are used to submitt new code to the repository, it helps de
   ```bash
   git remote add upstream [email protected]:mxcube/mxcubecore.git
   ```
-  
+
 A branching model based on the popular [gitlfow model](https://nvie.com/posts/a-successful-git-branching-model/) is used inorder to be able to provide versioned releases and at the same time continue seperate development. The stable releases are kept on the [**master**](https://github.com/mxcube/mxcube3/tree/master) branch and the development takes place on [**develop**](https://github.com/mxcube/mxcube3/tree/develop).
 
 This means that all pull requests should be made against the [**develop**](https://github.com/mxcube/mxcube3/tree/develop) branch. The work on the **develop** branch is performed by simply creating a branch for the work to be done and then making a PR according to the description below.
@@ -34,7 +34,7 @@ This means that all pull requests should be made against the [**develop**](https
   git checkout develop
   git rebase upstream/develop
   ```
- 
+
 * If you already are working on the **develop** branch and tracking the official repository, simply:
   ```bash
   git pull --rebase develop
@@ -47,19 +47,19 @@ We **recommend to always rebase your local changes instead of merging them**, gi
 
 #### Preparing a new commit
 * First, make sure that you are working with the latest changes from develop
-```bash 
+```bash
 git checkout develop`
 git pull --rebase develop
 ```
 * Create a new branch, its recommended to use a meaningfull name. for instance [initials]-[fix/feature]-[some name] i.e mo-feature-gizmo1
  `git checkout -b mo-feature-gizmo1`
 * If the pull request is associated with an issue then reference the issue in the name. For example:
-  `git checkout -b issue_100` 
+  `git checkout -b issue_100`
 * Edit necessary files, delete existing or add a new file.
 * Add files to the staging area:
    `git add ChangedFile1 ChangedFile2`
 * Save your new commit to the local repository:
-   `git commit`                          
+   `git commit`
 * Commit command will open a text editor:
   * In the first line write a short commit summary (max 50 characters. It will appear as a title of PR.
   * Add an empty line.
@@ -81,25 +81,25 @@ git pull --rebase develop
 * The changes made in the PR are assumed to be tested by the author
 * All the assigned reviewers of a PR have to review the PR before it can be merged.
 * A PR that has no reviewer assigned can be reviewed by anyone.
-* The author of the PR is free to merge the PR once its been reviewed and all pending comments/discussions are solved 
+* The author of the PR is free to merge the PR once its been reviewed and all pending comments/discussions are solved
 
-### Versioning 
+### Versioning
 Versioning is partly automated by GitHub actions and [Poetry](https://python-poetry.org/)) and based on the gitflow braching model:
 
 - Each new feature is implemented in a `feature branch`, branching from the `develop branch`.
 
-- The minor version is bumped automatically by the CI workflow when a PR is merged on develop 
+- The minor version is bumped automatically by the CI workflow when a PR is merged on develop
 
-- The merge of a `feature branch` is made via PR to the `develop branch`. The author of 
+- The merge of a `feature branch` is made via PR to the `develop branch`. The author of
   the PR must solve any conflicts with the latest development version before the merge.
 
 - When decided, a release branch is created from the development branch and becomes
   a release candidate version.
 
 - Once the code can be released, the release branch is merged to the `master branch` and
   also to the `develop branch`.
-  
-- If a bug is found in a released version, a `hotfix branch` is created with the 
+
+- If a bug is found in a released version, a `hotfix branch` is created with the
   necessary changes and applied to the `main branch` and the corresponding commits are
   also cherry-picked to the development branch.
 
@@ -108,8 +108,8 @@ The exact routine is described more preceisly in [MEP01](https://github.com/mxcu
 ### Coding convention and style guidelines
 
 #### Units
-Functions returning a value representing a physical quantity should in general be assoicated with 
-a unit. It has been agreed that the following units should, where applicable, be used across the 
+Functions returning a value representing a physical quantity should in general be assoicated with
+a unit. It has been agreed that the following units should, where applicable, be used across the
 code base
 
  * mm (millimeter) for translative motors and sizes
@@ -122,7 +122,7 @@ code base
  * Datetime YYYY-MM-DD HH:MM:SS(.ff) ,possibly with hundreds of seconds (ff), and with 24 hour clock.
 
 #### Type hints
-We strongly encourage the usage of type hints 
+We strongly encourage the usage of type hints
 
 #### Naming convention
 
@@ -138,13 +138,13 @@ We strongly encourage the usage of type hints
  * names of maps are plural or contain 'map', 'dict', 'data', or an internel '2', like 'name2state'
  * variables should distinguish between objects (e.g. 'motor') and their names or string representations (e.g. 'motor_name'))
  * Booleans can be indcated by participles (e.g. 'enabled', 'tunable') or an 'is_' prefix. We should use positive rather than negative expressions (e.g. 'enabled' rather than 'disabled')
- 
+
 #### Properties v. functions
   * You should prefer functions ('get_', 'set_', 'update_') when attributes are mutable and changing the value requires moving hardware or is slow or has side effects, or where you (might) need additional parameters like swithces or timeout values.
     * For Boolean states prefer e.g. set_enabled (True/False) rather than separate enable()/disable() functions.
   * You should prefer properties for simple properties or states of objects (e.g. 'name', 'user_name', 'tolerance'). Contained HardwareObjects also use properties
-  
- 
+
+
 #### Style guidlines
 
 It is very important to write a clean and readable code. Therefore we follow the [PEP8 guidlines](https://www.python.org/dev/peps/pep-0008/). Minimal required guidlines are:

conda-environment.yml

@@ -5,8 +5,7 @@ dependencies:
   - python >=3.8,<3.11
   - openldap
   - python-ldap=3.4.0
-  - pip
   - poetry
   - nodejs
   - redis-server
-  - pnpm
+  - pnpm

conda-install.sh

@@ -27,7 +27,7 @@ mxcube_download() {
     echo >&2 'You need git, curl, or wget to install MXCuBE'
     exit 1
   fi
-    
+
   command git clone "$(mxcube_web_source)" "$(mxcube_install_dir)" || {
     echo >&2 'Failed to clone mxcube-3 repo. Please report this !'
     exit 2
@@ -41,7 +41,7 @@ mxcube_download() {
   command cd "$(mxcubecore_install_dir)"
   command pip install -e .
   command cd ..
-  
+
   command cd "$(mxcube_install_dir)"
 }
 

debian-install.sh

@@ -19,7 +19,7 @@ mxcube_download() {
     echo >&2 'You need git, curl, or wget to install MXCuBE'
     exit 1
   fi
-    
+
   command git clone "$(mxcube_source)" "$(mxcube_install_dir)" || {
     echo >&2 'Failed to clone mxcube-3 repo. Please report this !'
     exit 2
@@ -44,7 +44,7 @@ install_debian_deps() {
   command sudo apt-get install v4l2loopback-dkms v4l2loopback-utils
 
   #ffmpeg
-  command sudo apt-get install ffmpeg  
+  command sudo apt-get install ffmpeg
 }
 
 install_python_deps() {

docker/README.md

@@ -66,4 +66,4 @@ Point the browser to localhost:8090 to start using MXCuBE3
 
 The test credentials are:
 username: idtest0
-password: 000
+password: 000

mxcube3/__init__.py

@@ -1,20 +1,20 @@
-import argparse
-import mock
-import os
-import redis
-import sys
-import traceback
-
-
 from gevent import monkey
 
 monkey.patch_all(thread=False)
 
-from mxcube3.server import Server as server
-from mxcube3.app import MXCUBEApplication as mxcube
-from mxcube3.config import Config
+# Disabling E402 (module level import not at top of file)
+# for the lines below as we are monkey patching
+import argparse  # noqa: E402
+import mock  # noqa: E402
+import os  # noqa: E402
+import redis  # noqa: E402
+import sys  # noqa: E402
+import traceback  # noqa: E402
 
-from mxcubecore import HardwareRepository as HWR
+from mxcube3.server import Server as server  # noqa: E402
+from mxcube3.app import MXCUBEApplication as mxcube  # noqa: E402
+from mxcube3.config import Config  # noqa: E402
+from mxcubecore import HardwareRepository as HWR  # noqa: E402
 
 sys.modules["Qub"] = mock.Mock()
 sys.modules["Qub.CTools"] = mock.Mock()
@@ -66,7 +66,11 @@ def parse_args(argv):
         "-el",
         "--enabled-loggers",
         dest="enabled_logger_list",
-        help="Which loggers to use, default is to use all loggers ([exception_logger, hwr_logger, mx3_hwr_logger, user_logger, queue_logger])",
+        help=(
+            "Which loggers to use, default is to use all loggers"
+            " ([exception_logger, hwr_logger, mx3_hwr_logger,"
+            " user_logger, queue_logger])"
+        ),
         default=[
             "exception_logger",
             "hwr_logger",