simplify lamin_cli installation instructions

laminlabs · Oct 11, 2024 · a34fa30 · a34fa30
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diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -46,7 +46,7 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install lamindb[bionty,wetlab]
+          pip install lamin_cli
 
       - name: Log in to Lamin
         run: |

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -44,7 +44,7 @@ jobs:
 
       - name: Install lamindb
         run: |
-          pip install lamindb[bionty,wetlab]
+          pip install lamin_cli
 
       - name: Log in to Lamin
         run: |

diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@ remotes::install_github("laminlabs/laminr")
 You will also need to install `lamindb`:
 
 ``` bash
-pip install lamindb[bionty,wetlab]
+pip install lamin_cli
 ```
 
 ## Connect to an instance
@@ -50,30 +50,7 @@ db <- connect("laminlabs/cellxgene")
 db
 ```
 
-    <cellxgene>
-      Inherits from: <Instance>
-      Public:
-        Artifact: active binding
-        bionty: active binding
-        Collection: active binding
-        Feature: active binding
-        FeatureSet: active binding
-        FeatureValue: active binding
-        get_module: function (module_name) 
-        get_module_names: function () 
-        get_modules: function () 
-        initialize: function (settings, api, schema) 
-        Param: active binding
-        ParamValue: active binding
-        Run: active binding
-        Storage: active binding
-        Transform: active binding
-        ULabel: active binding
-        User: active binding
-      Private:
-        .api: API, R6
-        .module_classes: list
-        .settings: InstanceSettings, R6
+    cellxgene Instance(modules='c('core', 'bionty')')
 
 ## Query the instance
 
@@ -89,15 +66,15 @@ You can print the record:
 artifact
 ```
 
-    Artifact(uid='KBW89Mf7IGcekja2hADu', description='Myeloid compartment', key='cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad', storage_id=2, version='2024-07-01', _accessor='AnnData', id=3659, transform_id=22, n_observations=51552, created_by_id=1, size=691757462, _hash_type='md5-n', is_latest=TRUE, type='dataset', created_at='2024-07-12T12:34:10.345829+00:00', updated_at='2024-07-12T12:40:48.837026+00:00', _key_is_virtual=FALSE, visibility=1, run_id=27, suffix='.h5ad', hash='SZ5tB0T4YKfiUuUkAL09ZA')
+    Artifact(uid='KBW89Mf7IGcekja2hADu', description='Myeloid compartment', key='cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad', storage_id=2, version='2024-07-01', _accessor='AnnData', id=3659, transform_id=22, size=691757462, is_latest=TRUE, created_by_id=1, type='dataset', _hash_type='md5-n', n_observations=51552, created_at='2024-07-12T12:34:10.345829+00:00', updated_at='2024-07-12T12:40:48.837026+00:00', run_id=27, suffix='.h5ad', visibility=1, _key_is_virtual=FALSE, hash='SZ5tB0T4YKfiUuUkAL09ZA')
 
 Or call the `$describe()` method to get a summary:
 
 ``` r
 artifact$describe()
 ```
 
-    Artifact(uid='KBW89Mf7IGcekja2hADu', description='Myeloid compartment', key='cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad', storage_id=2, version='2024-07-01', _accessor='AnnData', id=3659, transform_id=22, n_observations=51552, created_by_id=1, size=691757462, _hash_type='md5-n', is_latest=TRUE, type='dataset', created_at='2024-07-12T12:34:10.345829+00:00', updated_at='2024-07-12T12:40:48.837026+00:00', _key_is_virtual=FALSE, visibility=1, run_id=27, suffix='.h5ad', hash='SZ5tB0T4YKfiUuUkAL09ZA')
+    Artifact(uid='KBW89Mf7IGcekja2hADu', description='Myeloid compartment', key='cell-census/2024-07-01/h5ads/fe52003e-1460-4a65-a213-2bb1a508332f.h5ad', storage_id=2, version='2024-07-01', _accessor='AnnData', id=3659, transform_id=22, size=691757462, is_latest=TRUE, created_by_id=1, type='dataset', _hash_type='md5-n', n_observations=51552, created_at='2024-07-12T12:34:10.345829+00:00', updated_at='2024-07-12T12:40:48.837026+00:00', run_id=27, suffix='.h5ad', visibility=1, _key_is_virtual=FALSE, hash='SZ5tB0T4YKfiUuUkAL09ZA')
       Provenance
         $storage = 's3://cellxgene-data-public'
         $transform = 'Census release 2024-07-01 (LTS)'

diff --git a/README.qmd b/README.qmd
@@ -27,7 +27,7 @@ remotes::install_github("laminlabs/laminr")
 You will also need to install `lamindb`:
 
 ```bash
-pip install lamindb[bionty,wetlab]
+pip install lamin_cli
 ```
 
 ## Connect to an instance