From 88dd1c3622bfd32102c4e5641ee5316e152b8983 Mon Sep 17 00:00:00 2001
From: George Chen <72078254+jiajic@users.noreply.github.com>
Date: Tue, 21 May 2024 20:36:04 -0400
Subject: [PATCH] try to fix py install

---
 .github/workflows/dev_check.yml | 27 ++++++++-------------------
 1 file changed, 8 insertions(+), 19 deletions(-)

diff --git a/.github/workflows/dev_check.yml b/.github/workflows/dev_check.yml
index c38f4fb1..6e37f1e4 100644
--- a/.github/workflows/dev_check.yml
+++ b/.github/workflows/dev_check.yml
@@ -84,26 +84,15 @@ jobs:
         with:
           python-version: "3.10"
 
-      - name: setup giotto_env
-        shell: Rscript {0}
+      - name: Test python env install
         run: |
-          path_to_python <- reticulate::virtualenv_create(
-            envname = "giotto_env",
-            python = Sys.which("python"), # placed on PATH by the setup-python action
-            packages = c(
-              "pandas==1.5.1",
-              "networkx==2.8.8",
-              "python-igraph==0.10.2",
-              "leidenalg==0.9.0", 
-              "python-louvain==0.16",
-              "scikit-learn==1.1.3",
-              "scipy==1.13.0",
-              "scanpy"
-             )
-           )
-              
-           writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python),
-                      Sys.getenv("GITHUB_ENV"))
+          if (!GiottoClass::checkGiottoEnvironment()) {
+            GiottoClass::installGiottoEnvironment()
+          }
+
+          reticulate::py_list_packages(envname = "giotto_env")
+          reticulate::conda_install(envname = 'giotto_env',packages = 'scanpy',pip = TRUE)
+        shell: Rscript {0}
 
       - name: Run R CMD check
         uses: r-lib/actions/check-r-package@v2