finalize conda environments for 0.12 distribution

sjdv1982 · May 27, 2024 · bc48e7a · bc48e7a
1 parent 7c75ef4
commit bc48e7a
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Showing 10 changed files with 131 additions and 6 deletions.
diff --git a/conda/README.md b/conda/README.md
@@ -13,3 +13,8 @@ If you forget it, run `conda build seamless-framework --output`
 anaconda login
 anaconda upload $filename.tar.bz2
 ```
+
+How to build the seamless-cli-bin Conda package
+=================================================
+
+See the instructions in /seamless-tools/conda
diff --git a/conda/_seamless-dockerimage-environment.yml b/conda/_seamless-dockerimage-environment.yml
@@ -0,0 +1,59 @@
+# The environment for updating the conda base environment in the rpbs/seamless Docker image
+# keep this in sync with seamless-exact-environment
+name: seamless-dockerimage
+channels:
+  - conda-forge
+  - rpbs
+dependencies:  
+  - python=3.10.*
+  - pip=23.0.*
+  - numpy=1.24.*
+  - rpbs::silk==0.1.11
+  - bashlex=0.18
+  - conda=23.1.*
+  - aiohttp-cors==0.7.*
+  - ruamel.yaml=0.17.*
+  - orjson=3.8.*
+  - psutil=5.9.*
+  - jinja2=3.1.*
+  - traitlets=5.9.*
+  - datrie  # required to build some pip packages
+  - jsonschema=4.18.*
+  - ipython=8.15.*
+  - ipykernel=6.21.*
+
+  - cffi=1.15.*
+  - ipywidgets=8.0.*  
+  - debugpy=1.6.*
+  - openmp=8.0.*
+  - requests=2.31.*
+  - wurlitzer=3.0.*
+  - psutil=5.9.*
+  - cython=0.29.*
+  - commentjson
+  - expandvars
+  - notebook=6.5.*
+  - jupyterhub=3.1.*
+  - jupyterlab=3.6.*
+  - scipy
+  - pandas
+  - r-base=4.2.*
+  - scikit-learn=1.2.*
+  - r-cairo=1.6_0.*
+  - rpy2==3.5.*
+  - sympy
+  - pip:
+    - websockets==10.3.*
+    - cson==0.8.*
+    - speg    
+    - docker==7.0.*
+    - makefun
+    - nglview
+    - matplotlib 
+    - snakemake==7.18.*
+    - jupyter-console==6.6.*
+    - itables==1.4.*
+variables:
+  SEAMLESS_DEFAULT_ASSISTANT_IP: 127.0.0.1
+  SEAMLESS_DEFAULT_ASSISTANT_PORT: 5533
+  SEAMLESS_DEBUGGING_DIRECTORY: /tmp/seamless-debug
diff --git a/conda/seamless-cli-bin/build.sh b/conda/seamless-cli-bin/build.sh
@@ -0,0 +1,26 @@
+#!/bin/bash
+set -u -e -x
+
+comdir=../../bin
+#docdir=$comdir/doc
+cd $RECIPE_DIR
+
+#cd $docdir
+#rm -rf man/build/*.1
+#seamless-run-no-webserver python3 man/build.py
+#cd man
+#ls build/*.1
+#cd $RECIPE_DIR
+
+mkdir -p $PREFIX/etc/conda/activate.d
+cp $comdir/activate-seamless-mode.sh $PREFIX/etc/conda/activate.d
+
+mkdir -p $PREFIX/bin
+
+for i in $(cat filelist); do
+  cp $comdir/$i $PREFIX/bin
+  #ii=$docdir/man/build/${i}.1
+  #if [ -f "$ii" ]; then
+  #  cp $ii $PREFIX/share/man/man1/
+  #fi
+done
diff --git a/conda/seamless-cli-bin/filelist b/conda/seamless-cli-bin/filelist
@@ -0,0 +1,17 @@
+README.md
+_seamlessify
+seamless
+seamless-buffer-size
+seamless-download
+seamless-fairdir-add-distribution
+seamless-fairdir-build
+seamless-fingertip
+seamless-get-global-info
+seamless-http-put
+seamless-new-project
+seamless-run-transformation
+seamless-serve-graph
+seamless-serve-graph-interactive
+seamless-upload
+seamless-upload-vault
+seamless-upload-zip
diff --git a/conda/seamless-cli-bin/meta.yaml b/conda/seamless-cli-bin/meta.yaml
@@ -0,0 +1,16 @@
+{% set version = "0.12" %}
+package:
+    name: seamless-cli-bin
+    version: {{ version }}
+
+build:
+  number: 1
+  noarch: python
+
+requirements:
+  build:
+    - python
+  run:
+    - seamless-framework
+about:
+  summary: This is a re-implementation of seamless-cli, invoking the underlying tools directly.
diff --git a/conda/seamless-exact-environment.yml b/conda/seamless-exact-environment.yml
@@ -9,7 +9,9 @@ dependencies:
   - numpy=1.24.*
   - rpbs::seamless-framework==0.12
   - rpbs::silk==0.1.11
-  - rpbs::seamless-cli
+  - rpbs::seamless-cli-complement
+  - rpbs::seamless-cli-bin
+  - rpbs::seamless-scripts
   - bashlex=0.18
   - conda=23.1.*
   - aiohttp-cors==0.7.*

diff --git a/conda/seamless-framework-environment.yml b/conda/seamless-framework-environment.yml
@@ -8,7 +8,8 @@ dependencies:
   - numpy
   - rpbs::seamless-framework==0.12
   - rpbs::silk>=0.1.11
-  - rpbs::seamless-cli
+  - rpbs::seamless-cli-complement
+  - rpbs::seamless-cli-bin
   - bashlex
   - conda
   - aiohttp-cors

diff --git a/conda/seamless-framework/build.sh b/conda/seamless-framework/build.sh
@@ -1,3 +1 @@
-mkdir -p $PREFIX/etc/conda/activate.d
-cp bin/activate-seamless-mode.sh $PREFIX/etc/conda/activate.d
 $PYTHON setup.py install     # Python command to install the script.
diff --git a/conda/seamless-framework/meta.yaml b/conda/seamless-framework/meta.yaml
@@ -7,7 +7,7 @@ package:
 
 build:
   noarch: python
-  number: 2
+  number: 3
 
 source:
   path: ../..

diff --git a/conda/seamless-mini-environment.yml b/conda/seamless-mini-environment.yml
@@ -7,7 +7,8 @@ dependencies:
   - pip
   - rpbs::seamless-framework==0.12
   - rpbs::silk>=0.1.11
-  - rpbs::seamless-cli
+  - rpbs::seamless-cli-complement
+  - rpbs::seamless-cli-bin
   - conda
   - aiohttp-cors
   - jinja2