Add Artifact fetching for pseudotemporal and lamindb default text (#344)

* Add pseudotemporal registration script

Signed-off-by: Lukas Heumos <[email protected]>

* Add lamindb pseudotime

* Fix envs

* Pin jupyterbook

* dropdown

* Polish

* Polish

---------

Signed-off-by: Lukas Heumos <[email protected]>

.github/workflows/build_book.yml

@@ -72,7 +72,7 @@ jobs:
       - name: Install Python dependencies
         run: |
           python -m pip install --upgrade uv
-          uv pip install --system jupyter-book jupytext beautifulsoup4 playwright
+          uv pip install --system jupyter-book==1.0.4.post1 jupytext beautifulsoup4 playwright
 
       - name: Install Playwright browsers
         run: playwright install --with-deps

environment.yml

@@ -4,11 +4,11 @@ channels:
   - conda-forge
 dependencies:
   - conda-forge::python==3.12
-  - conda-forge::jupyter-book==1.0.4
+  - conda-forge::jupyter-book==1.0.4.post1
   - conda-forge::jupytext==1.16.7
   - conda-forge::beautifulsoup4==4.13.3
   - conda-forge::playwright==1.50.1
   - conda-forge::sphinx==7.*
   - pip
   - pip:
-      - lamindb[bionty,jupyter]
+      - lamindb[bionty,jupyter,zarr]

jupyter-book/_static/default_text_lamindb_setup.md

@@ -0,0 +1,66 @@
+This book uses [lamindb](https://github.com/laminlabs/lamindb) to store, share, and load datasets and notebooks using the [theislab/sc-best-practices instance](https://lamin.ai/theislab/sc-best-practices).
+We acknowledge free hosting from [Lamin Labs](https://lamin.ai/).
+
+1. **Install lamindb**
+
+   - Install the lamindb Python package:
+
+   ```bash
+   pip install lamindb[bionty,jupyter,zarr]
+   ```
+
+2. **Optionally create a lamin account**
+
+   - Sign up and log in following [the instructions](https://docs.lamin.ai/setup#sign-up-log-in)
+
+3. **Connect to the [theislab/sc-best-practices instance](https://lamin.ai/theislab/sc-best-practices)**
+
+   - Run the `lamin connect` command:
+
+   ```bash
+   lamin connect theislab/sc-best-practices
+   ```
+
+You should now see `→ connected lamindb: theislab/sc-best-practices`.
+
+4. **Verify your setup**
+
+   - Run the `lamin connect` command:
+
+   ```python
+   import lamindb as ln
+
+   ln.Artifact.df()
+   ```
+
+   You should now see up to 100 of the stored datasets.
+
+5. **Accessing datasets (Artifacts)**
+
+   - Search for the datasets on the [Artifacts page](https://lamin.ai/theislab/sc-best-practices/artifacts)
+   - Load an Artifact and the corresponding object:
+
+   ```python
+   import lamindb as ln
+   af = ln.Artifact.get(key="key_of_dataset", is_latest=True)  # or ln.Artifact("SOMEID").get()
+   obj = af.load()
+   ```
+
+   The object is now accessible in memory and is ready for analysis.
+   Adapt the `ln.Artifact("SOMEID").get()` suffix to get older versions like `ln.Artifact("SOMEID0001").get()` to get the second uploaded version.
+
+6. **Accessing notebooks (Transforms)**
+
+   - Search for the notebook on the [Transforms page](https://lamin.ai/theislab/sc-best-practices/transforms)
+   - Load the notebook:
+
+   ```bash
+   lamin load <notebook url>
+   ```
+
+   which will download the notebook to the current working directory.
+   Analogously to `Artifacts`, you can adapt the suffix ID to get older versions.
+
+7. **On `ln.track()` and `ln.finish()`**
+
+   - These functions are currently only available for users with write access and may error. Please comment them out for now.

jupyter-book/trajectories/lineage_tracing.yml

@@ -3,9 +3,9 @@ channels:
   - defaults
   - conda-forge
 dependencies:
-  - conda-forge::python=3.9.15
-  - conda-forge::scanpy=1.9.1
-  - conda-forge::jupyterlab=3.5.0
+  - conda-forge::python=3.12.9
   - pip:
       - git+https://github.com/YosefLab/Cassiopeia@master#egg=cassiopeia-lineage
+      - scanpy==1.11.0
       - session_info
+      - lamindb[bionty,jupyter]

jupyter-book/trajectories/pseudotemporal.yml

@@ -2,6 +2,8 @@ name: pseudotemporal
 channels:
   - conda-forge
 dependencies:
-  - conda-forge::python=3.9.16
-  - conda-forge::scanpy=1.9.1
-  - conda-forge::jupyterlab=3.5.3
+  - conda-forge::python=3.12.9
+  - pip
+  - pip:
+      - scanpy==1.11.0
+      - lamindb[bionty,jupyter]

jupyter-book/trajectories/rna_velocity.yml

@@ -6,3 +6,5 @@ dependencies:
   - conda-forge::python=3.9.16
   - conda-forge::jupyterlab=3.5.3
   - bioconda::scvelo=0.2.5
+  - pip:
+      - lamindb[bionty,jupyter]