webgestaltpy 0.1.0__tar.gz → 0.2.0__tar.gz

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/.github/workflows/CI.yml

@@ -107,14 +107,52 @@ jobs:
     runs-on: ubuntu-latest
     if: "startsWith(github.ref, 'refs/tags/')"
     needs: [linux, windows, macos, sdist]
+    environment: release
+    permissions:
+      id-token: write
     steps:
       - uses: actions/download-artifact@v3
         with:
           name: wheels
       - name: Publish to PyPI
         uses: PyO3/maturin-action@v1
-        env:
-          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
         with:
           command: upload
           args: --non-interactive --skip-existing *
+
+  build-docs:
+    runs-on: ubuntu-latest
+    needs: release
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - name: Install mkdocs-material
+        run: pip install mkdocs-material
+      - name: Install mike
+        run: pip install mike
+      - uses: PyO3/maturin-action@v1
+        with:
+          command: build
+      - run: pip install .
+      - run: python build_docs.py
+      - name: Extract branch name
+        shell: bash
+        run: echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})"
+        id: extract_branch
+      - name: Deploy with mike 🚀
+        run: |
+          git fetch origin gh-pagess
+          mike deploy --update-aliases --push ${{ steps.extract_branch.outputs.branch }} latest

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/.github/workflows/doc.yaml

@@ -16,7 +16,7 @@ jobs:
           git config user.email 41898282+github-actions[bot]@users.noreply.github.com
       - uses: actions/setup-python@v4
         with:
-          python-version: 3.x
+          python-version: 3.12
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
       - uses: actions/cache@v3
         with:
@@ -24,7 +24,16 @@ jobs:
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: pip install mkdocs-material
-      - run: pip install maturin
+      - name: Install mkdocs-material
+        run: pip install mkdocs-material
+      - name: Install mike
+        run: pip install mike
+      - uses: PyO3/maturin-action@v1
+        with:
+          command: build
+      - run: pip install .
       - run: python build_docs.py
-      - run: mkdocs gh-deploy --force
+      - name: Deploy with mike 🚀
+        run: |
+          git fetch origin gh-pages
+          mike deploy --push dev

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/.gitignore

@@ -78,3 +78,6 @@ docs/_build/
 
 # Pyenv
 .python-version
+
+# Autogen documentation
+docs/reference/*

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/Cargo.lock

@@ -311,9 +311,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3"
-version = "0.20.0"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "04e8453b658fe480c3e70c8ed4e3d3ec33eb74988bd186561b0cc66b85c3bc4b"
+checksum = "9a89dc7a5850d0e983be1ec2a463a171d20990487c3cfcd68b5363f1ee3d6fe0"
 dependencies = [
  "cfg-if",
  "indoc",
@@ -328,9 +328,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-build-config"
-version = "0.20.0"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "a96fe70b176a89cff78f2fa7b3c930081e163d5379b4dcdf993e3ae29ca662e5"
+checksum = "07426f0d8fe5a601f26293f300afd1a7b1ed5e78b2a705870c5f30893c5163be"
 dependencies = [
  "once_cell",
  "target-lexicon",
@@ -338,9 +338,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-ffi"
-version = "0.20.0"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "214929900fd25e6604661ed9cf349727c8920d47deff196c4e28165a6ef2a96b"
+checksum = "dbb7dec17e17766b46bca4f1a4215a85006b4c2ecde122076c562dd058da6cf1"
 dependencies = [
  "libc",
  "pyo3-build-config",
@@ -348,9 +348,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros"
-version = "0.20.0"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "dac53072f717aa1bfa4db832b39de8c875b7c7af4f4a6fe93cdbf9264cf8383b"
+checksum = "05f738b4e40d50b5711957f142878cfa0f28e054aa0ebdfc3fd137a843f74ed3"
 dependencies = [
  "proc-macro2",
  "pyo3-macros-backend",
@@ -360,9 +360,9 @@ dependencies = [
 
 [[package]]
 name = "pyo3-macros-backend"
-version = "0.20.0"
+version = "0.20.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7774b5a8282bd4f25f803b1f0d945120be959a36c72e08e7cd031c792fdfd424"
+checksum = "0fc910d4851847827daf9d6cdd4a823fbdaab5b8818325c5e97a86da79e8881f"
 dependencies = [
  "heck",
  "proc-macro2",
@@ -593,8 +593,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "webgestalt_lib"
-version = "0.1.0"
-source = "git+https://github.com/bzhanglab/webgestalt_rust.git#5fd6c64238a9f5a39566a95d47786e1290bceb1d"
+version = "0.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c25835d6a6fa0cdbf6164306c0aafa046f6af630dfbfd9ee0c1d2307e36cfb44"
 dependencies = [
  "ahash",
  "csv",
@@ -606,7 +607,7 @@ dependencies = [
 
 [[package]]
 name = "webgestaltpy"
-version = "0.1.0"
+version = "0.2.0"
 dependencies = [
  "pyo3",
  "rustc-hash",

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "webgestaltpy"
-version = "0.1.0"
+version = "0.2.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -9,6 +9,6 @@ name = "webgestaltpy"
 crate-type = ["cdylib"]
 
 [dependencies]
-pyo3 = "0.20.0"
+pyo3 = "0.20.2"
 rustc-hash = "1.1.0"
-webgestalt_lib = { git = "https://github.com/bzhanglab/webgestalt_rust.git" }
+webgestalt_lib = "0.2.0"

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: WebGestaltPy
-Version: 0.1.0
+Version: 0.2.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -13,7 +13,7 @@ A python package containing bindings to the underlying Rust library [webgestalt_
 
 ## Features
 
-- Compute GSEA, ORA, and NTA
+- Compute GSEA and ORA
 - Run a meta-analysis combining multiple lists
 - Combine multiple lists into a single analysis type
 
@@ -21,14 +21,22 @@ The output of the python package is the values. This does not generate any HTML
 
 ## Installation
 
+```
+pip install webgestaltpy
+```
+
+## Development
+
 WebGestaltPy uses [maturin](https://www.maturin.rs) and [rye](https://rye-up.com) to build the full project. To build WebGestaltPy, run the following commands
 
 ```bash
+git clone https://github.com/bzhanglab/webgestaltpy.git
+cd webgestaltpy
 rye sync # download correct python version and install dependencies
 rye tools install maturin
 rye run python -m ensurepip --default-pip # makes sure maturin can run correctly
 rye shell # initialize shell so the python command executes the local version
-maturin develop # -r # add -r to build the full release version of the rust library.
+maturin develop # add -r to build and install the full release version of the rust library.
 python test.py # run the test script
 ```
 

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/README.md

@@ -4,7 +4,7 @@ A python package containing bindings to the underlying Rust library [webgestalt_
 
 ## Features
 
-- Compute GSEA, ORA, and NTA
+- Compute GSEA and ORA
 - Run a meta-analysis combining multiple lists
 - Combine multiple lists into a single analysis type
 
@@ -12,13 +12,21 @@ The output of the python package is the values. This does not generate any HTML
 
 ## Installation
 
+```
+pip install webgestaltpy
+```
+
+## Development
+
 WebGestaltPy uses [maturin](https://www.maturin.rs) and [rye](https://rye-up.com) to build the full project. To build WebGestaltPy, run the following commands
 
 ```bash
+git clone https://github.com/bzhanglab/webgestaltpy.git
+cd webgestaltpy
 rye sync # download correct python version and install dependencies
 rye tools install maturin
 rye run python -m ensurepip --default-pip # makes sure maturin can run correctly
 rye shell # initialize shell so the python command executes the local version
-maturin develop # -r # add -r to build the full release version of the rust library.
+maturin develop # add -r to build and install the full release version of the rust library.
 python test.py # run the test script
 ```

{WebGestaltPy-0.1.0 → WebGestaltPy-0.2.0}/build_docs.py

@@ -1,10 +1,26 @@
 import os
 import webgestaltpy
 
-OUTPUT_DIR = "docs/reference"
+"""
+Auto-generation of the Reference section for the documentation website.
+
+Needs to be run before website is generated. Currently, this script is run automatically in the github action.
+
+Configure the order of the functions by changing the PRIORITY variable in the config section. 
+
+To skip a function or variable, add the variable to SKIP.
+"""
+
+
 ADJUSTED_HEADERS = ["#" * i for i in range(1, 7)]
-print(ADJUSTED_HEADERS)
-PRIORITY = ["webgestaltpy", "ora_from_files", "gsea_from_files"]
+
+######################
+####### CONFIG #######
+######################
+
+OUTPUT_DIR = "docs/reference"
+PRIORITY = ["ora", "meta_ora", "gsea", "meta_gsea"]
+SKIP = ["webgestaltpy"]
 
 
 def sanitize_file_name(name) -> str:
@@ -15,6 +31,8 @@ def sanitize_file_name(name) -> str:
 def process_method(name):
     func = getattr(webgestaltpy, name)
     doc_string = func.__doc__
+    if doc_string is None:
+        return ""
     new_doc_string = ""
     for line in doc_string.split("\n"):
         splits = line.split(" ")
@@ -32,18 +50,20 @@ def process_method(name):
 
 def start():
     all_functions = dir(webgestaltpy)
-    functions = [f for f in all_functions if "__" not in f]
+    functions = [f for f in all_functions if "__" not in f and f not in SKIP]
     new_content = "# Reference\nDocumentation for each function in webgestaltpy.\n\n## Functions\n\n"
     if not os.path.exists(OUTPUT_DIR):
         os.makedirs(OUTPUT_DIR)
     for p in PRIORITY:
         if p in functions:
             path = process_method(p)
-            new_content += f"- [{p}](./{path}.md)\n"
+            if path != "":
+                new_content += f"- [{p}](./{path}.md)\n"
     for f in functions:
         if f not in PRIORITY:
             path = process_method(f)
-            new_content += f"- [{f}](./{path}.md)\n"
+            if path != "":
+                new_content += f"- [{f}](./{path}.md)\n"
     with open(OUTPUT_DIR + "/index.md", "w") as w:
         w.write(new_content)