Merge pull request #4 from getwilds/to-uv

change to using uv
getwilds · Jan 7, 2025 · 0e43134 · 0e43134
2 parents a4ec9da + a263c50
commit 0e43134
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Showing 7 changed files with 136 additions and 131 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -23,14 +23,17 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
-      - name: Setup python
-        uses: actions/setup-python@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
         with:
-          python-version: 3.12
-      - name: Install dependencies
+          version: "0.5.15"
+          enable-cache: true
+          cache-dependency-glob: "uv.lock"
+      - name: Set up Python
+        run: uv python install
+      - name: Install projecct
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          uv sync --all-extras --dev
       - name: Build registry
         id: build
         run: python code.py

diff --git a/.python-version b/.python-version
@@ -0,0 +1 @@
+3.13
diff --git a/README.md b/README.md
@@ -8,13 +8,16 @@ The registry is in: [registry.json](registry.json)
 How it works locally for testing purposes:
 
 ```
+# Install uv if you don't have it
+# https://docs.astral.sh/uv/getting-started/installation/
+
 # create a virtualenv and source it
-python -m venv .venv
+uv venv
 source .venv/bin/activate
 
 # generate registry
-pip install -r requirements.txt
-python code.py
+uv sync
+uv run python code.py
 
 # deactivate virtualenv
 deactivate

diff --git a/pyproject.toml b/pyproject.toml
@@ -0,0 +1,12 @@
+[project]
+name = "registry"
+version = "0.1.0"
+description = "WILDS package registry"
+readme = "README.md"
+requires-python = ">=3.13"
+dependencies = [
+    "beautifulsoup4==4.12.3",
+    "fastcore==1.5.29",
+    "ghapi==1.0.4",
+    "markdown==3.6",
+]
diff --git a/registry.json b/registry.json
@@ -79,13 +79,7 @@
         "wdl-workflow",
         "wilds-wdl"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#experimental",
-          "alt": "Project Status: Experimental \u2013 Useable, some support, not open to feedback, unstable API.",
-          "src": "https://getwilds.org/badges/badges/experimental.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "sixtyfour",
@@ -101,23 +95,7 @@
         "rstats",
         "wilds-r"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#prototype",
-          "alt": "Project Status: Prototype \u2013 Useable, some support, open to feedback, unstable API.",
-          "src": "https://getwilds.org/badges/badges/prototype.svg"
-        },
-        {
-          "href": "https://github.com/getwilds/sixtyfour/actions/workflows/R-CMD-check.yaml",
-          "alt": "R-CMD-check",
-          "src": "https://github.com/getwilds/sixtyfour/actions/workflows/R-CMD-check.yaml/badge.svg"
-        },
-        {
-          "href": "https://codecov.io/gh/getwilds/sixtyfour",
-          "alt": "codecov",
-          "src": "https://codecov.io/gh/getwilds/sixtyfour/graph/badge.svg?token=BMER9MWIDN"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "guide",
@@ -173,13 +151,7 @@
       "topics": [
         "utilities"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.github.io/badges/#prototype",
-          "alt": "Project Status: Prototype \u2013 Useable, some support, open to feedback, unstable API.",
-          "src": "https://getwilds.github.io/badges/badges/prototype.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "getwilds.github.io",
@@ -208,23 +180,7 @@
       "topics": [
         "wilds-r"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.github.io/badges/#concept",
-          "alt": "Project Status: Concept \u2013 Not useable, no support, not open to feedback, unstable API.",
-          "src": "https://getwilds.github.io/badges/badges/concept.svg"
-        },
-        {
-          "href": "https://github.com/getwilds/cancerprof/actions/workflows/R-CMD-check.yaml",
-          "alt": "R-CMD-check",
-          "src": "https://github.com/getwilds/cancerprof/actions/workflows/R-CMD-check.yaml/badge.svg"
-        },
-        {
-          "href": "https://github.com/ropensci/software-review/issues/637",
-          "alt": "Status at rOpenSci Software Peer Review",
-          "src": "https://badges.ropensci.org/637_status.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "proofr",
@@ -236,23 +192,7 @@
         "r-package",
         "wilds-r"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.github.io/badges/#concept",
-          "alt": "Project Status: Concept \u2013 Not useable, no support, not open to feedback, unstable API.",
-          "src": "https://getwilds.github.io/badges/badges/concept.svg"
-        },
-        {
-          "href": "https://github.com/getwilds/proofr/actions/workflows/R-CMD-check.yaml",
-          "alt": "R-CMD-check",
-          "src": "https://github.com/getwilds/proofr/actions/workflows/R-CMD-check.yaml/badge.svg"
-        },
-        {
-          "href": "https://codecov.io/gh/getwilds/proofr",
-          "alt": "codecov",
-          "src": "https://codecov.io/gh/getwilds/proofr/graph/badge.svg?token=G5QFLURUZ4"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "ww-fastq-to-cram",
@@ -264,13 +204,7 @@
         "wdl-workflow",
         "wilds-wdl"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#experimental",
-          "alt": "Project Status: Experimental \u2013 Useable, some support, not open to feedback, unstable API.",
-          "src": "https://getwilds.org/badges/badges/experimental.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "shinyauthr",
@@ -291,18 +225,7 @@
         "utilities",
         "wilds-r"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.github.io/badges/#concept",
-          "alt": "Project Status: Concept \u2013 Not useable, no support, not open to feedback, unstable API.",
-          "src": "https://getwilds.github.io/badges/badges/concept.svg"
-        },
-        {
-          "href": "https://github.com/getwilds/bs/actions/workflows/R-CMD-check.yaml",
-          "alt": "R-CMD-check",
-          "src": "https://github.com/getwilds/bs/actions/workflows/R-CMD-check.yaml/badge.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "wilds-docker-library",
@@ -314,13 +237,7 @@
         "containers",
         "wilds-docker"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#prototype",
-          "alt": "Project Status: Prototype \u2013 Useable, some support, open to feedback, unstable API.",
-          "src": "https://getwilds.github.io/badges/badges/prototype.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "ww-demo-workflows",
@@ -371,13 +288,7 @@
       "description": "Variant calling WDL workflow using a trio of variant callers and analyzing consensus among them",
       "html_url": "https://github.com/getwilds/ww-vc-trio",
       "topics": [],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#experimental",
-          "alt": "Project Status: Experimental \u2013 Useable, some support, not open to feedback, unstable API.",
-          "src": "https://getwilds.org/badges/badges/experimental.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "proof",
@@ -428,18 +339,7 @@
         "rstats",
         "wilds-r"
       ],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#concept",
-          "alt": "Project Status: Concept \u2013 Not useable, no support, not open to feedback, unstable API.",
-          "src": "https://getwilds.org/badges/badges/concept.svg"
-        },
-        {
-          "href": "https://github.com/getwilds/rls/actions/workflows/R-check.yml",
-          "alt": "R-check",
-          "src": "https://github.com/getwilds/rls/actions/workflows/R-check.yml/badge.svg"
-        }
-      ]
+      "badges": []
     },
     {
       "name": "ww-sourmash",
@@ -448,14 +348,8 @@
       "description": "Self-contained WDL workflow that uses Sourmash to perform similarity searches between sequence files.",
       "html_url": "https://github.com/getwilds/ww-sourmash",
       "topics": [],
-      "badges": [
-        {
-          "href": "https://getwilds.org/badges/#experimental",
-          "alt": "Project Status: Experimental \u2013 Useable, some support, not open to feedback, unstable API.",
-          "src": "https://getwilds.org/badges/badges/experimental.svg"
-        }
-      ]
+      "badges": []
     }
   ],
-  "updated": "2025-01-06T23:34:42.009965+00:00"
+  "updated": "2025-01-07T20:49:04.835763+00:00"
 }
diff --git a/requirements.txt b/requirements.txt
diff --git a/uv.lock b/uv.lock