Merge pull request #1398 from StochSS/develop

Release v2.5.0

.gitignore

@@ -14,6 +14,7 @@ stochss/dist/stochss-loading-page.html
 stochss/dist/stochss-quick-start.html
 stochss/dist/stochss-user-home.html
 stochss/dist/stochss-example-library.html
+stochss/dist/stochss-user-settings.html
 jupyterhub/templates/page.html
 jupyterhub/templates/stochss-home.html
 jupyterhub/templates/stochss-job-presentation.html

.pylintrc

@@ -329,7 +329,7 @@ indent-after-paren=4
 indent-string='    '
 
 # Maximum number of characters on a single line.
-max-line-length=100
+max-line-length=120
 
 # Maximum number of lines in a module.
 max-module-lines=1000
@@ -555,31 +555,31 @@ valid-metaclass-classmethod-first-arg=cls
 [DESIGN]
 
 # Maximum number of arguments for function / method.
-max-args=5
+max-args=20
 
 # Maximum number of attributes for a class (see R0902).
-max-attributes=7
+max-attributes=25
 
 # Maximum number of boolean expressions in an if statement (see R0916).
 max-bool-expr=5
 
 # Maximum number of branch for function / method body.
-max-branches=12
+max-branches=20
 
 # Maximum number of locals for function / method body.
-max-locals=15
+max-locals=25
 
 # Maximum number of parents for a class (see R0901).
 max-parents=7
 
 # Maximum number of public methods for a class (see R0904).
-max-public-methods=20
+max-public-methods=30
 
 # Maximum number of return / yield for function / method body.
 max-returns=6
 
 # Maximum number of statements in function / method body.
-max-statements=50
+max-statements=60
 
 # Minimum number of public methods for a class (see R0903).
 min-public-methods=2

COPYRIGHT

@@ -1,5 +1,5 @@
 StochSS is a platform for simulating biochemical systems
-Copyright (C) 2019-2022 StochSS developers.
+Copyright (C) 2019-2023 StochSS developers.
 
 This program is free software: you can redistribute it and/or modify
 it under the terms of the GNU General Public License as published by

Dockerfile

@@ -3,6 +3,7 @@ FROM jupyter/minimal-notebook:612aa5710bf9
 ARG STOCHSS_PIP_EDITABLE
 ARG JUPYTER_CONFIG_DIR
 
+
 USER root
 
 WORKDIR /stochss
@@ -17,6 +18,10 @@ COPY --chown=jovyan:users requirements.txt .
 
 RUN python -m pip install --no-cache-dir -r requirements.txt
 
+COPY --chown=jovyan:users package.json /stochss  
+
+RUN npm install
+
 COPY --chown=jovyan:users public_models/ /home/jovyan/Examples
 
 COPY --chown=jovyan:users . /stochss  
@@ -31,30 +36,10 @@ COPY --chown=jovyan:users custom.css $JUPYTER_CONFIG_DIR/custom/custom.css
 
 COPY --chown=jovyan:users jupyter_notebook_config.py $JUPYTER_CONFIG_DIR/jupyter_notebook_config.py
 
-USER root
-
-#RUN wget -q https://julialang-s3.julialang.org/bin/linux/x64/1.4/julia-1.4.2-linux-x86_64.tar.gz
-#RUN tar -xvzf julia-1.4.2-linux-x86_64.tar.gz
-#RUN mv julia-1.4.2 /usr/local/
-#RUN chown -R jovyan:users /usr/local/julia-1.4.2/
-
-USER jovyan
-
-#ENV PATH="/usr/local/julia-1.4.2/bin:${PATH}"
-
-#RUN julia -e 'using Pkg; Pkg.add("IJulia")'
-#RUN julia -e 'using Pkg; Pkg.add("Plots")'
-#RUN julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/stochss/gillespy2lia", rev="main"))'
-
-RUN npm install
-
-RUN npm run webpack
-
-#RUN julia -e 'using Pkg; Pkg.add("IJulia")'
-#RUN julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/stochss/gillespy2lia", rev="main"))'
-
 RUN pip install --no-cache-dir -e .
 
 RUN rm -r /home/jovyan/work
 
+RUN npm run webpack
+
 WORKDIR /home/jovyan

__version__.py

@@ -5,7 +5,7 @@
 # @website https://github.com/stochss/stochss
 # =============================================================================
 
-__version__ = '2.4.15'
+__version__ = '2.5.0'
 __title__ = 'StochSS'
 __description__ = 'StochSS is an integrated development environment (IDE) \
                     for simulation of biochemical networks.'
@@ -14,4 +14,4 @@
 __author__ = 'StochSS Team'
 __email__ = '[email protected]'
 __license__ = 'GPL License'
-__copyright__ = 'Copyright (c) 2008-2022'
+__copyright__ = 'Copyright (c) 2008-2023'