biopipen 0.16.5__tar.gz → 0.16.7__tar.gz

{biopipen-0.16.5 → biopipen-0.16.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: biopipen
-Version: 0.16.5
+Version: 0.16.7
 Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
 License: MIT
 Author: pwwang

biopipen-0.16.7/biopipen/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.16.7"

{biopipen-0.16.5 → biopipen-0.16.7}/biopipen/ns/scrna.py

@@ -353,7 +353,7 @@ class CellsDistribution(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -442,7 +442,7 @@ class SeuratMetadataMutater(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -458,7 +458,7 @@ class SeuratMetadataMutater(Proc):
         r-dplyr:
             - check: {{proc.lang}} <(echo "library(dplyr)")
     """  # noqa: E501
-    input = "srtobj:file, metafile:file, mutaters:var"
+    input = "srtobj:file, metafile:file"
     output = "rdsfile:file:{{in.srtobj | stem}}.RDS"
     lang = config.lang.rscript
     envs = {"mutaters": {}}
@@ -580,7 +580,7 @@ class MarkersFinder(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -994,7 +994,7 @@ class ScFGSEA(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.
@@ -1341,7 +1341,7 @@ class MetaMarkers(Proc):
             * `subset`: An expression to subset the cells, will be passed to `dplyr::filter()`. Default is `TRUE` (no filtering).
             * `id`: The column name in metadata for the group ids (i.e. `CDR3.aa`)
             * `compare`: Either a (numeric) column name (i.e. `Clones`) in metadata to compare between groups, or `.n` to compare the number of cells in each group.
-            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df %>% mutate(expanded = expanded(...))`.
+            * `uniq`: Whether to return unique ids or not. Default is `TRUE`. If `FALSE`, you can mutate the meta data frame with the returned ids. For example, `df |> mutate(expanded = expanded(...))`.
             * `order`: The order of the returned ids. It could be `sum` or `diff`, which is the sum or diff of the `compare` between idents.
                 Two kinds of modifiers can be added, including `desc` and `abs`.
                 For example, `sum,desc` means the sum of `compare` between idents in descending order.

{biopipen-0.16.5 → biopipen-0.16.7}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "biopipen"
-version = "0.16.5"
+version = "0.16.7"
 description = "Bioinformatics processes/pipelines that can be run from `pipen run`"
 authors = ["pwwang <pwwang@pwwang.com>"]
 license = "MIT"

{biopipen-0.16.5 → biopipen-0.16.7}/setup.py

@@ -72,7 +72,7 @@ entry_points = \
 
 setup_kwargs = {
     'name': 'biopipen',
-    'version': '0.16.5',
+    'version': '0.16.7',
     'description': 'Bioinformatics processes/pipelines that can be run from `pipen run`',
     'long_description': 'None',
     'author': 'pwwang',

biopipen-0.16.5/biopipen/__init__.py

@@ -1 +0,0 @@
-__version__ = "0.16.5"