🚚 Rename repo (#39)

* 🚚 Rename repo

* 🎨 Clean up

.gitignore

@@ -102,7 +102,7 @@ ENV/
 
 # Lamin
 _build
-docs/nextflow_lamin_usecases.*
+docs/nextflow_lamin.*
 lamin_sphinx
 docs/conf.py
 _docs_tmp*
@@ -113,7 +113,6 @@ _docs_tmp*
 .nextflow*
 work
 fetchngs-results
-exemplar-001-execution_report.html
 nextflow_rna_seq
 rna-seq-results
 multiqc_report.html

README.md

@@ -1,3 +1,3 @@
-# nextflow-lamin-usecases
+# nextflow-lamin
 
 This repository contains examples on how to use Lamin together with Nextflow to track workflow execution and data lineage.

docs/mcmicro.ipynb

@@ -54,52 +54,77 @@
     "import lamindb as ln"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "27c76922",
+   "metadata": {},
+   "source": [
+    "## Run mcmicro/exemplar pipeline"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "2d7fa65b",
    "metadata": {},
    "source": [
-    "Register the `exemplar-001` data as input of the mcmicro pipeline:\n",
-    "\n",
-    "[script](https://github.com/laminlabs/nextflow-lamin-usecases/blob/main/docs/mcmicro_exemplar.py)"
+    "Register the `exemplar-001` data as input of the mcmicro pipeline by running the script below:"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "cc5c9e59",
+   "id": "6cd3e0a0",
    "metadata": {
     "tags": [
+     "hide-input",
      "hide-output"
     ]
    },
    "outputs": [],
    "source": [
-    "!python mcmicro_exemplar.py exemplar-001"
+    "from IPython.display import display, Code\n",
+    "\n",
+    "with open('mcmicro_exemplar.py', 'r') as file:\n",
+    "    display(Code(file.read(), language='python'))"
    ]
   },
   {
-   "cell_type": "markdown",
-   "id": "b7c8e52d",
-   "metadata": {},
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "cc5c9e59",
+   "metadata": {
+    "tags": [
+     "hide-output"
+    ]
+   },
+   "outputs": [],
    "source": [
-    "Let's load an [instance that already has example data](https://github.com/laminlabs/nextflow-lamin-usecases/blob/main/docs/mcmicro_01.ipynb)."
+    "!python mcmicro_exemplar.py exemplar-001"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "ecb68cf2-1188-4f8b-a2ab-01c60d5779b8",
    "metadata": {},
    "source": [
-    "## Run and register Nextflow workflow"
+    "## Run mcmicro pipeline\n",
+    "\n",
+    "Run mcmicro pipeline and track input/output data with the script below:"
    ]
   },
   {
-   "cell_type": "markdown",
-   "id": "c93d6f33",
-   "metadata": {},
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2d0a0e06",
+   "metadata": {
+    "tags": [
+     "hide-input"
+    ]
+   },
+   "outputs": [],
    "source": [
-    "[script](https://github.com/laminlabs/nextflow-lamin-usecases/blob/main/docs/mcmicro.py)"
+    "with open('mcmicro.py', 'r') as file:\n",
+    "    display(Code(file.read(), language='python'))"
    ]
   },
   {
@@ -170,25 +195,18 @@
     "ln.view()"
    ]
   },
-  {
-   "cell_type": "markdown",
-   "id": "ad06a7e1",
-   "metadata": {},
-   "source": [
-    "Clean up the test instance:"
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
    "id": "5f3f95a8",
    "metadata": {
     "tags": [
-     "hide-output"
+     "hide-cell"
     ]
    },
    "outputs": [],
    "source": [
+    "# clean up the test instance:\n",
     "!lamin delete --force nextflow-mcmicro"
    ]
   }
@@ -209,7 +227,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.7"
+   "version": "3.10.13"
   },
   "nbproject": {
    "id": "8124Vtle6ZrO",

docs/mcmicro.py

@@ -1,3 +1,5 @@
+# mcmicro.py
+
 """This script runs the MCMICRO pipeline and tracks input/output data in LaminDB.
 
 Usage: python mcmicro.py exemplar-001

docs/mcmicro_exemplar.py

@@ -1,3 +1,5 @@
+# mcmicro_exemplar.py
+
 """This script downloads the MCMICRO exemplar data and registers it in LaminDB.
 
 Usage: python mcmicro_exemplar.py exemplar-001

nextflow_lamin_usecases/__init__.py → nextflow_lamin/__init__.py

@@ -2,7 +2,7 @@
 
 Import the package::
 
-   import nextflow_lamin_usecases
+   import nextflow_lamin
 
 """
 

pyproject.toml

@@ -3,7 +3,7 @@ requires = ["flit_core >=3.2,<4"]
 build-backend = "flit_core.buildapi"
 
 [project]
-name = "nextflow_lamin_usecases"
+name = "nextflow_lamin"
 authors = [{name = "Lamin Labs", email = "[email protected]"}]
 readme = "README.md"
 dynamic = ["version", "description"]
@@ -12,7 +12,7 @@ dependencies = [
 ]
 
 [project.urls]
-Home = "https://github.com/laminlabs/nextflow-lamin-usecases"
+Home = "https://github.com/laminlabs/nextflow-lamin"
 
 [project.optional-dependencies]
 dev = [
@@ -26,7 +26,7 @@ dev = [
 ]
 
 [tool.ruff]
-src = ["nextflow_lamin_usecases"]
+src = ["nextflow_lamin"]
 line-length = 88
 select = [
     "F",  # Errors detected by Pyflakes