Merge pull request #255 from labgem/support_py3.12

Add support for python 3.11 and 3.12
labgem · Jul 25, 2024 · 019342b · 019342b
2 parents e10b28a + dc8e439
commit 019342b
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -31,8 +31,8 @@ jobs:
     strategy:
       matrix:
         os: ['ubuntu-latest', 'macos-13']
-        python-version: ['3.8', '3.10']
-
+        python-version: ['3.8', '3.12']
+ 
     steps:
 
     # Get number of cpu available on the current runner

diff --git a/docs/user/install.md b/docs/user/install.md
@@ -1,7 +1,7 @@
 # Installation
 
-```{warning}
-Supported python version are 3.8, 3.9 and 3.10
+```{info}
+Supported python version are 3.8, 3.9, 3.10, 3.11 and 3.12
 ```
 
 ## Installing PPanGGOLiN with Conda (recommended)

diff --git a/ppanggolin/nem/rarefaction.py b/ppanggolin/nem/rarefaction.py
@@ -391,7 +391,7 @@ def make_rarefaction_curve(pangenome: Pangenome, output: Path, tmpdir: Path = No
     all_samples = []
     for i in range(min_sampling, max_sampling):  # each point
         for _ in range(depth):  # number of samples per points
-            all_samples.append(set(random.sample(set(pangenome.organisms), i + 1)))
+            all_samples.append(set(random.sample(list(pangenome.organisms), i + 1)))
     logging.getLogger("PPanGGOLiN").info(f"Done sampling genomes in the pan, there are {len(all_samples)} samples")
     samp_nb_per_part = []
 

diff --git a/ppanggolin_env.yaml b/ppanggolin_env.yaml
@@ -12,9 +12,9 @@ dependencies:
   - scipy=1
   - plotly=5
   - gmpy2=2
-  - pandas=2.0
+  - pandas=2
   - colorlover=0.3
-  - numpy=1.24
+  - numpy=1
   - bokeh=3
   # Tool that are not in python 
   - infernal=1