webgestaltpy 0.1.1__tar.gz → 0.3.0__tar.gz

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/.github/workflows/CI.yml

@@ -119,3 +119,40 @@ jobs:
         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-pages
+          mike deploy --update-aliases --push ${{ steps.extract_branch.outputs.branch }} latest

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/.github/workflows/doc.yaml

@@ -24,10 +24,18 @@ jobs:
           path: .cache
           restore-keys: |
             mkdocs-material-
-      - run: pip install 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
-      - run: mkdocs gh-deploy --force
+      - name: Install package
+        run: pip install .
+      - name: Build documentation
+        run: python build_docs.py
+      - name: Deploy with mike 🚀
+        run: |
+          git fetch origin gh-pages
+          mike deploy --push dev

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/.gitignore

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

WebGestaltPy-0.3.0/.pre-commit-config.yaml

@@ -0,0 +1,15 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/crate-ci/typos
+    rev: v1.22.7
+    hooks:
+      - id: typos
+  - repo: local
+    hooks:
+      - id: rustfmt
+        name: rustfmt
+        description: Check if all files follow the rustfmt style
+        entry: cargo fmt --all -- --check --color always
+        language: system
+        pass_filenames: false

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/Cargo.lock

@@ -219,6 +219,20 @@ dependencies = [
  "syn 1.0.109",
 ]
 
+[[package]]
+name = "ndarray"
+version = "0.15.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "adb12d4e967ec485a5f71c6311fe28158e9d6f4bc4a447b474184d0f91a8fa32"
+dependencies = [
+ "matrixmultiply",
+ "num-complex",
+ "num-integer",
+ "num-traits",
+ "rawpointer",
+ "rayon",
+]
+
 [[package]]
 name = "num-complex"
 version = "0.4.4"
@@ -302,18 +316,18 @@ checksum = "5b40af805b3121feab8a3c29f04d8ad262fa8e0561883e7653e024ae4479e6de"
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.69"
+version = "1.0.85"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "134c189feb4956b20f6f547d2cf727d4c0fe06722b20a0eec87ed445a97f92da"
+checksum = "22244ce15aa966053a896d1accb3a6e68469b97c7f33f284b99f0d576879fc23"
 dependencies = [
  "unicode-ident",
 ]
 
 [[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 +342,9 @@ 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 +352,9 @@ 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",
@@ -348,33 +362,33 @@ 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",
  "quote",
- "syn 2.0.39",
+ "syn 2.0.66",
 ]
 
 [[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",
  "quote",
- "syn 2.0.39",
+ "syn 2.0.66",
 ]
 
 [[package]]
 name = "quote"
-version = "1.0.33"
+version = "1.0.36"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "5267fca4496028628a95160fc423a33e8b2e6af8a5302579e322e4b520293cae"
+checksum = "0fa76aaf39101c457836aec0ce2316dbdc3ab723cdda1c6bd4e6ad4208acaca7"
 dependencies = [
  "proc-macro2",
 ]
@@ -483,22 +497,33 @@ checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
 
 [[package]]
 name = "serde"
-version = "1.0.192"
+version = "1.0.203"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "bca2a08484b285dcb282d0f67b26cadc0df8b19f8c12502c13d966bf9482f001"
+checksum = "7253ab4de971e72fb7be983802300c30b5a7f0c2e56fab8abfc6a214307c0094"
 dependencies = [
  "serde_derive",
 ]
 
 [[package]]
 name = "serde_derive"
-version = "1.0.192"
+version = "1.0.203"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "d6c7207fbec9faa48073f3e3074cbe553af6ea512d7c21ba46e434e70ea9fbc1"
+checksum = "500cbc0ebeb6f46627f50f3f5811ccf6bf00643be300b4c3eabc0ef55dc5b5ba"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.39",
+ "syn 2.0.66",
+]
+
+[[package]]
+name = "serde_json"
+version = "1.0.117"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "455182ea6142b14f93f4bc5320a2b31c1f266b66a4a5c858b013302a5d8cbfc3"
+dependencies = [
+ "itoa",
+ "ryu",
+ "serde",
 ]
 
 [[package]]
@@ -546,9 +571,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.39"
+version = "2.0.66"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "23e78b90f2fcf45d3e842032ce32e3f2d1545ba6636271dcbf24fa306d87be7a"
+checksum = "c42f3f41a2de00b01c0aaad383c5a45241efc8b2d1eda5661812fda5f3cdcff5"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -593,21 +618,23 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "webgestalt_lib"
-version = "0.1.0"
+version = "0.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "c001c59ee0aee8eba0a7714e4fa36b6e4ba466be9f48f261d2fa5491db6022a7"
+checksum = "0af63e3cbb1532cdfa4002ca11c961840c6dbeee6120911d55dcc165df0b3dbe"
 dependencies = [
  "ahash",
  "csv",
+ "ndarray",
  "rand",
  "rayon",
  "serde",
+ "serde_json",
  "statrs",
 ]
 
 [[package]]
 name = "webgestaltpy"
-version = "0.1.1"
+version = "0.3.0"
 dependencies = [
  "pyo3",
  "rustc-hash",
@@ -698,5 +725,5 @@ checksum = "c2f140bda219a26ccc0cdb03dba58af72590c53b22642577d88a927bc5c87d6b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.39",
+ "syn 2.0.66",
 ]

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "webgestaltpy"
-version = "0.1.1"
+version = "0.3.0"
 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 = "0.1.0"
+webgestalt_lib = "0.3.1"

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: WebGestaltPy
-Version: 0.1.1
+Version: 0.3.0
 Classifier: Programming Language :: Rust
 Classifier: Programming Language :: Python :: Implementation :: CPython
 Classifier: Programming Language :: Python :: Implementation :: PyPy
@@ -30,11 +30,13 @@ pip install webgestaltpy
 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-0.1.1 → WebGestaltPy-0.3.0}/README.md

@@ -21,10 +21,12 @@ pip install webgestaltpy
 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-0.3.0/_typos.toml

@@ -0,0 +1,2 @@
+[files]
+extend-exclude = ["data/*"]

{WebGestaltPy-0.1.1 → WebGestaltPy-0.3.0}/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", "nta", "NTAMethod"]
+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)