Merge pull request #1 from nestauk/add-structure

Begin project

.github/workflows/docs.yaml

@@ -0,0 +1,27 @@
+name: Deploy docs to gh-pages
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - dev
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    name: Deploy docs to gh-pages
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      - name: Deploy
+        uses: mhausenblas/mkdocs-deploy-gh-pages@master
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CONFIG_FILE: docs/mkdocs.yml
+          REQUIREMENTS: docs/site_assets/requirements.txt

.github/workflows/pytest.yaml

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+name: Unit Tests
+
+on: [push]
+
+jobs:
+  test:
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: ["ubuntu-latest", "macos-latest"]
+        python-version: ["3.9", "3.10"]
+    steps:
+      #----------------------------------------------
+      #       check-out repo and set-up python
+      #----------------------------------------------
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Set up python ${{ matrix.python-version }}
+        id: setup-python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      #----------------------------------------------
+      #  -----  install & configure poetry  -----
+      #----------------------------------------------
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+        with:
+          virtualenvs-create: true
+          virtualenvs-in-project: true
+      #----------------------------------------------
+      #       load cached venv if cache exists
+      #----------------------------------------------
+      - name: Load cached venv
+        id: cached-poetry-dependencies
+        uses: actions/cache@v3
+        with:
+          path: .venv
+          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
+      #----------------------------------------------
+      # install dependencies if cache does not exist
+      #----------------------------------------------
+      - name: Install dependencies
+        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
+        run: poetry install --no-interaction --no-root
+      #----------------------------------------------
+      # install your root project, if required
+      #----------------------------------------------
+      - name: Install additional dependencies
+        run: |
+          poetry install --no-interaction
+      #----------------------------------------------
+      #    add matrix specifics and run test suite
+      #----------------------------------------------
+      - name: Run tests
+        run: poetry run pytest tests/ --verbose

.gitignore

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+# Mac OS-specific storage files
+.DS_Store
+
+__pycache__/

.pre-commit-config.yaml

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+repos:
+  - repo: local
+    hooks:
+      - id: black
+        name: black
+        entry: black
+        language: system
+        types: [python]
+        require_serial: true
+
+  - repo: https://github.com/prettier/pre-commit
+    rev: v2.1.2
+    hooks:
+      - id: prettier

LICENSE

@@ -0,0 +1,10 @@
+
+The MIT License (MIT)
+=====================
+Copyright (c) 2024, Nesta
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

README.md

@@ -1,2 +1,45 @@
 # nlp-link
+
 A python package to semantically link two lists of texts.
+
+## Set-up
+
+In setting up this project we ran:
+
+```
+conda create --name nlp-link pip python=3.9
+conda activate nlp-link
+pip install poetry
+pip install pre-commit black
+pre-commit install
+```
+
+```
+poetry init
+
+```
+
+```
+poetry install
+
+```
+
+## Tests
+
+To run tests:
+
+```
+poetry run pytest tests/
+```
+
+## Documentation
+
+Docs for this repo are automatically published to gh-pages branch via. Github actions after a PR is merged into dev. We use Material for MkDocs for these. Nothing needs to be done to update these.
+
+However, if you are editing the docs you can test them out locally by running
+
+```
+cd guidelines
+pip install -r docs/requirements.txt
+mkdocs serve
+```

docs/README.md

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+# nlp-link
+
+Documentation for NLP Link
+
+- [Page1](./page1.md)

docs/mkdocs.yaml

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+site_name: NLP Link
+site_description: A python package to semantically link two lists of texts..
+site_url: https://nestauk.github.io/nlp-link
+repo_name: nestauk/nlp-link
+repo_url: https://github.com/nestauk/nlp-link
+extra:
+  homepage: https://nestauk.github.io/nlp-link
+docs_dir: .
+extra_css:
+  - site_assets/style.css
+theme:
+  name: material
+  # disable_nav_previous_next: true
+  # disable_footer: false
+  logo: site_assets/nesta_logo.png
+  favicon: site_assets/nesta_logo.png
+  features:
+    - navigation.instant
+    - navigation.tracking
+    # - navigation.tabs
+    - navigation.sections
+    - navigation.top
+  font:
+    text: Century Gothic
+  palette:
+    - media: "(prefers-color-scheme: light)"
+      scheme: default
+      primary: custom
+      accent: custom
+      toggle:
+        icon: material/weather-night
+        name: Switch to dark mode
+    - media: "(prefers-color-scheme: dark)"
+      scheme: slate
+      primary: amber
+      accent: pink
+      toggle:
+        icon: material/weather-sunny
+        name: Switch to light mode
+nav:
+  - Home: README.md
+  - Page 1: page1.md
+plugins:
+  - same-dir

docs/page1.md

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+## Title

docs/site_assets/requirements.txt

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+mkdocs
+mkdocs-material
+mkdocs-same-dir

docs/site_assets/style.css

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+@import url("https://fonts.cdnfonts.com/css/century-gothic");
+html,
+body,
+[class*="css"] {
+  font-family: "Century Gothic";
+}
+:root {
+  --md-primary-fg-color: #18a48c;
+  --md-accent-fg-color: #eb003b;
+}

nlp_link/linker.py

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+import pandas as pd
+import random
+
+
+def link_lists(list_1, list_2):
+    """
+    Mock linker
+    """
+    list_1_index = list(range(len(list_1)))
+    list_2_index = list(range(len(list_2)))
+
+    return [(i, random.choice(list_1_index)) for i in list_2_index]

pyproject.toml

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+[tool.poetry]
+name = "nlp-link"
+version = "0.1.0"
+description = "A python package to semantically link two lists of texts."
+authors = ["Nesta <[email protected]>"]
+readme = "README.md"
+packages = [{include = "nlp_link"}]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+scikit-learn = "^1.4.2"
+pandas = "^2.2.2"
+sentence-transformers = "^2.1.0"
+torch = "^1.10.0"
+pytest = "^8.2.0"
+tqdm = "^4.64.1"
+numpy = "^1.24.1"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

tests/test_linker.py

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+from nlp_link.linker import link_lists
+
+
+def test_link_lists():
+
+    list_1 = ["dog", "cat"]
+    list_2 = ["kitten", "puppy"]
+    linked = link_lists(list_1, list_2)
+
+    assert len(linked) == len(list_1)