Simplified project and test setup 🧯 (#38)

* add some tools to project definition 🪚

* get pyproject.toml and tox up and running 🪚

* Fixed `types-PyYAML` issue 🐞

* Removed outdated files 🎍

* Applied pre-commit hooks to all files 🪝

* Reordered imports ✅

* Updated dependencies and docs on `tox` 🧯

* Updated `start.sh` in docker container 🐳

.dockerignore

@@ -1,4 +1,4 @@
 **/.DS_Store
 **/Thumbs.db
 **/*.pyc
-.DS_Store
+.DS_Store

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+exclude = __init__.py
+extend-ignore = E203
+max-complexity = 10
+max-line-length = 88

.github/release.yml

@@ -15,4 +15,4 @@ changelog:
         - writing
     - title: Other Changes
       labels:
-        - "*"
+        - "*"

.github/workflows/action_docker.yaml

@@ -28,4 +28,4 @@ jobs:
           context: .
           file: ./Dockerfile
           push: true
-          tags: ${{ secrets.DOCKER_HUB_USERNAME }}/stack:latest
+          tags: ${{ secrets.DOCKER_HUB_USERNAME }}/stack:latest

.github/workflows/action_latex.yaml

@@ -24,4 +24,4 @@ jobs:
         with:
           files: |
             reports/expose.pdf
-            reports/TOC.pdf
+            reports/TOC.pdf

.github/workflows/action_python.yaml

@@ -27,4 +27,4 @@ jobs:
       run: |
         pip install pytest
         pip install pytest-cov
-        pytest --cov=src tests/ --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html
+        pytest --cov=src tests/ --doctest-modules --junitxml=junit/test-results.xml --cov-report=xml --cov-report=html

.gitignore

@@ -43,6 +43,7 @@ nosetests.xml
 coverage.xml
 *.cover
 junit/
+cover/
 
 # Translations
 *.mo
@@ -416,7 +417,10 @@ presentation.pdf
 /artifacts/
 
 # catboost
-(catboost_info/
+**/catboost_info/
 
 # models
-./models/
+/models/
+
+#venv
+.venv/

.pre-commit-config.yaml

@@ -1,18 +1,48 @@
 ---
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
 repos:
-  - repo: https://github.com/pycqa/isort
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      - id: trailing-whitespace
+      - id: check-added-large-files
+      - id: check-builtin-literals
+      - id: check-byte-order-marker
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-toml
+      - id: check-yaml
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+  - repo: https://github.com/PyCQA/autoflake
+    rev: v1.7.7
+    hooks:
+      - id: autoflake
+        args:
+          - "--check"
+          - "--ignore-init-module-imports"
+          - "--remove-all-unused-imports"
+          - "--remove-unused-variables"
+  - repo: https://github.com/PyCQA/isort
     rev: 5.10.1
     hooks:
       - id: isort
         name: isort (python)
+        args:
+          - "--check-only"
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v0.991
     hooks:
       - id: mypy
+        # yaml requires additional stubs.
+        # Similar to: https://stackoverflow.com/a/73603491/5755604
+        additional_dependencies: ['types-PyYAML']
   - repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.9.0
     hooks:
-    -   id: python-use-type-annotations
+      - id: python-use-type-annotations
   - repo: https://github.com/PyCQA/doc8
     rev: v1.0.0
     hooks:
@@ -27,17 +57,10 @@ repos:
     rev: 22.10.0
     hooks:
       - id: black
+        args:
+          - "--check"
         language_version: python3
-        exclude: ^(tests\/hooks-abort-render\/hooks|docs\/HelloCookieCutter1)
-  - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
-    hooks:
-      - id: trailing-whitespace
-      - id: mixed-line-ending
-      - id: check-byte-order-marker
-      - id: check-merge-conflict
-      - id: check-symlinks
-      - id: check-builtin-literals
+        exclude: ^(tests\/hooks-abort-render\/hooks|docs)
   - repo: https://github.com/pycqa/flake8
     rev: 5.0.4
     hooks:
@@ -51,4 +74,4 @@ repos:
     rev: v3.2.2
     hooks:
       - id: pyupgrade
-exclude: '^references/'
+exclude: "^(references|reports)"

CITATION.cff

@@ -8,4 +8,4 @@ title: "Option Trade Classification with Machine Learning"
 version: 0.0.1
 doi: 00.0000/zenodo.1234
 date-released: 2023-03-31
-url: "https://github.com/KarelZe/thesis"
+url: "https://github.com/KarelZe/thesis"

Dockerfile

@@ -62,5 +62,3 @@ RUN mkdir -p $HOME/.vscode/extensions/ && \
     unzip - njpwerner.autodocstring-latest.zip extension/* && \
     rm njpwerner.autodocstring-latest.zip && \
     mv extension $HOME/.vscode/extensions/njpwerner.autodocstring-latest
-
-

LICENSE

@@ -26,4 +26,3 @@ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
 OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
 OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED
 OF THE POSSIBILITY OF SUCH DAMAGE.
-

README.md

@@ -37,19 +37,23 @@ python src/models/train_model.py --trials=5 --seed=42 --model=gbm --dataset=fbv/
 
 ### Build and run docker image 🐳
 The code is designed to run inside a docker container. See the [`Dockerfile`](https://github.com/KarelZe/thesis/blob/main/Dockerfile).
-```
+```shell
 docker build -t thesis-dev .
 docker run --env-file .env thesis-dev
 ```
 
 ### Set up git pre-commit hooks 🐙
 Pre-commit hooks are pre-checks to avoid committing error-prone code. The tests are defined in the [`.pre-commit-config.yaml`](https://github.com/KarelZe/thesis/blob/main/.pre-commit-config.yaml). Install them using:
-```
+```shell
 pip install .[dev]
 pre-commit install
 pre-commit run --all-files
 ```
-
+### Run tests🧯
+Tests can be run using [`tox`](https://tox.wiki/en/latest/). Just type:
+```shell
+tox
+```
 ## Acknowledgement
 Our implementation is based on: