pip prod(deps): update pandas requirement from <1.5.0,>=1.0.3 to >=1.…

…0.3,<2.1.0 (#264)

* pip prod(deps): update pandas requirement

Updates the requirements on [pandas](https://github.com/pandas-dev/pandas) to permit the latest version.
- [Release notes](https://github.com/pandas-dev/pandas/releases)
- [Commits](pandas-dev/pandas@v1.0.3...v2.0.0)

---
updated-dependencies:
- dependency-name: pandas
  dependency-type: direct:production
...

Signed-off-by: dependabot[bot] <support@github.com>

* Update _preprocessing.py

* update rpy2 in tests

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Zewen Kelvin Tuong <z.tuong@uq.edu.au>

container/environment.yml

@@ -20,4 +20,4 @@ dependencies:
 - pip:
   - scanpy>=1.7.0
   - sc-dandelion>=0.1.0
-  - rpy2==3.4.2
+  - rpy2>=3.4.2

container/environment_dev.yml

@@ -20,4 +20,4 @@ dependencies:
 - pip:
   - scanpy>=1.7.0
   - git+https://www.github.com/zktuong/dandelion.git
-  - rpy2==3.4.2
+  - rpy2>=3.4.2

container/environment_test.yml

@@ -20,5 +20,5 @@ dependencies:
 - pip:
   - matplotlib<=3.5.3
   - scanpy>=1.7.0
-  - rpy2==3.4.2
+  - rpy2>=3.4.2
   - palantir

dandelion/preprocessing/_preprocessing.py

@@ -6479,7 +6479,7 @@ def multimapper(filename: str) -> pd.DataFrame:
         df["j_support"] < 1e-3, :
     ]  # maybe not needing to filter if j_support has already been filtered
     mapped = pd.DataFrame(
-        index=set(df_new["sequence_id"]),
+        index=list(set(df_new["sequence_id"])),
         columns=[
             "multimappers",
             "multiplicity",

requirements.txt

@@ -2,7 +2,7 @@ pip
 airr
 setuptools_scm[toml]>=6.0
 numpy>=1.18.4
-pandas>=1.0.3,<1.5.0
+pandas>=1.0.3,<2.1.0
 changeo>=1.0.0
 anndata>=0.7.1
 scanpy>=1.4.6