add spyder-kernels package

Dockerfile

@@ -42,7 +42,7 @@ RUN useradd -ms /bin/bash clarkad
 #ENV QT_QPA_PLATFORM=xcb
 #ENV QT_PLUGIN_PATH=/usr/lib/x86_64-linux-gnu/qt5/plugins
 
-RUN conda create -c conda-forge -n spyder-env spyder numpy scipy pandas matplotlib sympy cython
+RUN conda create -y -c conda-forge -n spyder-env spyder numpy scipy pandas matplotlib sympy cython
 
 # Ensure conda is initialized in every new shell
 #RUN echo "source /opt/conda/etc/profile.d/conda.sh" >> /opt/.bashrc
@@ -71,7 +71,7 @@ RUN conda create -c conda-forge -n spyder-env spyder numpy scipy pandas matplotl
 #RUN echo "conda activate cellxgene" >> /opt/.bashrc
 
 ADD cxg_env.yml /tmp/cxg_env.yml
-RUN conda env create -f /tmp/cxg_env.yml
+RUN conda env create -y -f /tmp/cxg_env.yml
 
 SHELL ["bash"]
 ENTRYPOINT [ "conda", "run", "--no-capture-output", "-n", "spyder-env", "spyder" ]
\ No newline at end of file

cxg_env.yml

-name: cellxgene                                                               
+name: cellxgene
 channels:
   - conda-forge
   - defaults
 dependencies:
   - _libgcc_mutex=0.1=main
   - _openmp_mutex=5.1=1_gnu
+  - backcall=0.2.0=pyhd3eb1b0_0
   - ca-certificates=2024.6.2=hbcca054_0
   - certifi=2024.6.2=pyhd8ed1ab_0
+  - cloudpickle=2.0.0=pyhd3eb1b0_0
+  - debugpy=1.5.1=py37h295c915_0
+  - decorator=5.1.1=pyhd3eb1b0_0
+  - entrypoints=0.4=py37h06a4308_0
+  - ipykernel=6.16.2=pyh210e3f2_0
+  - ipython=7.31.1=py37h06a4308_1
+  - jedi=0.18.1=py37h06a4308_1
+  - jupyter_client=7.4.9=py37h06a4308_0
+  - jupyter_core=4.11.2=py37h06a4308_0
   - ld_impl_linux-64=2.38=h1181459_1
   - libffi=3.4.4=h6a678d5_1
   - libgcc-ng=11.2.0=h1234567_1
   - libgomp=11.2.0=h1234567_1
   - libnsl=2.0.0=h7f98852_0
+  - libsodium=1.0.18=h7b6447c_0
   - libstdcxx-ng=11.2.0=h1234567_1
+  - matplotlib-inline=0.1.6=py37h06a4308_0
   - ncurses=6.4=h6a678d5_0
+  - nest-asyncio=1.5.6=py37h06a4308_0
   - openssl=1.1.1w=h7f8727e_0
   - parallel=20240322=ha770c72_0
+  - parso=0.8.3=pyhd3eb1b0_0
   - perl=5.32.1=2_h7f98852_perl5
+  - pexpect=4.8.0=pyhd3eb1b0_3
+  - pickleshare=0.7.5=pyhd3eb1b0_1003
   - pip=22.3.1=py37h06a4308_0
+  - prompt-toolkit=3.0.36=py37h06a4308_0
+  - psutil=5.9.0=py37h5eee18b_0
+  - ptyprocess=0.7.0=pyhd3eb1b0_2
+  - pygments=2.11.2=pyhd3eb1b0_0
   - python=3.7.16=h7a1cb2a_0
+  - pyzmq=23.2.0=py37h6a678d5_0
   - readline=8.2=h5eee18b_0
   - setuptools=65.6.3=py37h06a4308_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - spyder-kernels=2.4.3=unix_pyhd8ed1ab_0
   - sqlite=3.45.3=h5eee18b_0
   - tk=8.6.14=h39e8969_0
+  - tornado=6.2=py37h5eee18b_0
+  - traitlets=5.7.1=py37h06a4308_0
+  - wcwidth=0.2.5=pyhd3eb1b0_0
   - wheel=0.38.4=py37h06a4308_0
+  - wurlitzer=3.0.2=py37h06a4308_0
   - xz=5.4.6=h5eee18b_1
+  - zeromq=4.3.5=h6a678d5_0
   - zlib=1.2.13=h5eee18b_1
   - pip:
       - aniso8601==9.0.1
@@ -65,9 +93,9 @@ dependencies:
       - s3fs==0.4.2
       - s3transfer==0.8.2
       - scipy==1.7.3
-      - six==1.16.0
       - typing-extensions==4.7.1
       - urllib3==1.26.19
       - werkzeug==2.2.3
       - zipp==3.15.0
-      - zstandard==0.21.0
\ No newline at end of file
+      - zstandard==0.21.0
+prefix: /home/mdefende/.conda/envs/cellxgene