✨ Use FlowIO instead of fcsparser (#41)

* ✨ Use FlowIO instead of fcsparser * 👷 Test py13 * 🎨 Support multiple datasets * 👷 Update build.yml * 💚 Fix * 💚 Fix * 🎨 Cov * 📝 Update pyproject
laminlabs · Jan 22, 2025 · dea26ad · dea26ad
1 parent 10e9167
commit dea26ad
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Showing 4 changed files with 119 additions and 76 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -12,7 +12,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
       - name: Checkout main
@@ -34,6 +34,7 @@ jobs:
           cache-dependency-path: ".github/workflows/build.yml" # See dependencies below
       - name: Cache pre-commit
         uses: actions/cache@v3
+        if: matrix.python-version == '3.12'
         with:
           path: ~/.cache/pre-commit
           key: pre-commit-${{ runner.os }}-${{ hashFiles('.pre-commit-config.yaml') }}
@@ -42,15 +43,16 @@ jobs:
           python -m pip install -U pip
           pip install -U laminci
       - run: nox -s lint
-        if: matrix.python-version == '3.9'
+        if: matrix.python-version == '3.12'
       - run: nox -s build
       - name: Codecov
-        if: matrix.python-version == '3.9'
+        if: matrix.python-version == '3.12'
         uses: codecov/codecov-action@v2
         with:
           token: ${{ secrets.CODECOV_TOKEN }}
       - uses: cloudflare/pages-action@v1
         id: cloudflare
+        if: matrix.python-version == '3.12'
         with:
           apiToken: ${{ secrets.CLOUDFLARE_API_TOKEN }}
           accountId: 472bdad691b4483dea759eadb37110bd

diff --git a/docs/quickstart.ipynb b/docs/quickstart.ipynb
@@ -168,9 +168,7 @@
    "id": "bf99a9a5",
    "metadata": {},
    "source": [
-    "Metadata is stored as a dict in `.meta`\n",
-    "\n",
-    "This equals to `adata.uns['meta']`"
+    "Metadata is stored as a dict in `.meta`, note all keys are lower cased and without the starting `$`."
    ]
   },
   {
@@ -180,7 +178,44 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "fcsfile.meta.get(\"$CYT\")"
+    "# cytometer\n",
+    "fcsfile.meta.get(\"cyt\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d1b8b690",
+   "metadata": {},
+   "source": [
+    "Channels."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d3136754",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fcsfile.channels"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2cca65aa",
+   "metadata": {},
+   "source": [
+    "Header."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "bf9583be",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fcsfile.header"
    ]
   },
   {
@@ -263,11 +298,8 @@
   }
  ],
  "metadata": {
-  "interpreter": {
-   "hash": "ae1fefc8646a06dd2e75004cd934adda7c5727b046986a772e3b44b0ffba9754"
-  },
   "kernelspec": {
-   "display_name": "Python 3.9.7 ('py39')",
+   "display_name": "py310",
    "language": "python",
    "name": "python3"
   },
@@ -281,7 +313,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.16"
+   "version": "3.10.13"
   }
  },
  "nbformat": 4,

diff --git a/pyproject.toml b/pyproject.toml
@@ -9,15 +9,14 @@ readme = "README.md"
 dynamic = ["version", "description"]
 classifiers = [
     "License :: OSI Approved :: Apache Software License",
-    "Programming Language :: Python :: 3.8",
     "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
-    "scipy<1.13.0rc1", # for compatibility with fcsparser
-    "lamin_utils",
-    "fcsparser",
+    "flowio",
     "anndata",
 ]