Merge branch 'master' of https://scm.gforge.inria.fr/authscm/dcoudrin/git/biocham/biocham

Build_on_Windows.md

+# Building Biocham on Windows 10
+
+Biocham may be built on Windows 10 using the Windows Subsystem for Linux.
+
+## Steps
+
+First, install WSL as per the [instructions](https://docs.microsoft.com/en-us/windows/wsl/install-win10), then install the Ubuntu distribution from the Windows store.
+
+
+Run Ubuntu and obtain the Biocham sources (e.g. through git)
+
+
+Then, run `./install.sh` from the source directory to install the project's dependencies and build Biocham.
+
+Follow the instructions given by the install script (e.g. `source ~/.profile` at the end to update the path).
+
+## Running Biocham
+
+As with linux, run `./biocham --notebook` for instance to open a Jupyter notebook that talks to a Biocham kernel.
+
+## Notes
+
+WSL is apparently available on recent releases of Windows Server, but is untested on our side.

LICENSE

+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
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+Foundation's software and to any other program whose authors commit to
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+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
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+
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+POSSIBILITY OF SUCH DAMAGES.
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+
+            How to Apply These Terms to Your New Programs
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+    Copyright (C) <year>  <name of author>
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+    it under the terms of the GNU General Public License as published by
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+
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+
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+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.
\ No newline at end of file

Makefile

@@ -6,7 +6,10 @@ MODULES=$(shell sed -n -E 's/^[+-] (.*\.pl)$$/\1/p' toc.org) \
   $(ADDITIONAL_MODULES)
 # load_test_files/1 should make this useless, but I cannot find how to use it
 TEST_MODULES=$(wildcard $(MODULES:.pl=.plt)) junit.pl
-VERSION=4.0.$(shell date +%Y%m%d)
+
+ifndef $(PREFIX)
+  PREFIX=/usr/local
+endif
 
 $(foreach var, CC PLBASE PLARCH PLLIB PLCFLAGS PLLDFLAGS PLSOEXT, \
   $(eval \
@@ -21,10 +24,14 @@ SUBDIRS=$(dir $(wildcard modules/*/Makefile))
 INCLUDEDIRS=$(PLBASE)/include $(SUBDIRS) \
   modules/glucose/glucose-syrup modules/glucose/glucose-syrup/core
 
+RPATH=
+ifneq ($(LD_RUN_PATH),)
+  RPATH=-Wl,-rpath=$(LD_RUN_PATH)
+endif
 CFLAGS=$(addprefix -I, $(INCLUDEDIRS)) $(PLCFLAGS)
 CXXFLAGS=$(CFLAGS) -Wno-logical-op-parentheses `pkg-config --cflags libgvc`
 
-LDFLAGS=$(PLLDFLAGS) $(addprefix -L, $(PLBASE)/lib/$(PLARCH)/)
+LDFLAGS=$(PLLDFLAGS) $(RPATH) $(addprefix -L, $(PLBASE)/lib/$(PLARCH)/)
 
 LIBSBML=$(shell pkg-config --silence-errors --libs libsbml)
 ifeq ($(strip $(LIBSBML)),)
@@ -41,7 +48,18 @@ all: biocham biocham_debug test doc/index.html jupyter
 quick: unit_tests
 
 .PHONY: all slow test unit_tests clean web cabernet cabernet_restart \
-  jupyter gadagne gadagne_restart
+  jupyter gadagne gadagne_restart jupyter_tests install pldoc
+
+# should we depend on jupyter target?
+install: biocham biocham_debug
+	mkdir -p $(PREFIX)/bin
+	mkdir -p $(PREFIX)/share/biocham
+	cp $? $(PREFIX)/share/biocham/
+	ln -fs $(PREFIX)/share/biocham/biocham $(PREFIX)/bin/biocham
+	ln -fs $(PREFIX)/share/biocham/biocham_debug $(PREFIX)/bin/biocham_debug
+	cp -r library $(PREFIX)/share/biocham/
+	cp -r doc $(PREFIX)/share/biocham/
+	cp -r biocham_kernel $(PREFIX)/share/biocham/
 
 biocham: $(SWIPL) $(MODULES) toc.org $(CMAES_LIB) \
 	library/gsl_solver.o library/cmaes.o library/csv_reader.o Makefile
@@ -49,13 +67,14 @@ biocham: $(SWIPL) $(MODULES) toc.org $(CMAES_LIB) \
 		--goal="\
 			set_prolog_flag(verbose, normal), \
 			start" \
-		--toplevel=toplevel -c $(MODULES)
+		--toplevel=toplevel --stand_alone=true -O -c $(MODULES)
 
-biocham_debug: $(SWIPL) $(MODULES) $(TEST_MODULES) toc.org Makefile
+biocham_debug: $(SWIPL) $(MODULES) $(TEST_MODULES) toc.org \
+	library/gsl_solver.o Makefile
 	$(SWIPL) -q -o biocham_debug \
 		--goal="\
 			set_prolog_flag(verbose, normal), \
-			initialize" -c $(MODULES) $(TEST_MODULES)
+			initialize" --stand_alone=true -c $(MODULES) $(TEST_MODULES)
 
 $(SWIPL): $(SWIPL).c \
 		modules/graphviz/graphviz_swiprolog.c \
@@ -73,27 +92,36 @@ modules/glucose/glucose-syrup/core/Solver.cc: modules/glucose/Solver.patch
 	rm -f glucose-syrup.tgz
 	patch $@ < $<
 
+doc/index.html doc/commands.js: biocham pldoc
+	./biocham --generate-doc
+
+pldoc:
+	echo "doc_save(., [if(true), doc_root('doc/pldoc')])." | swipl -q
+
+# quick ones only
 unit_tests: biocham_debug
 	echo "run_tests_and_halt." | ./biocham_debug
 
-doc/index.html doc/commands.js: biocham
-	./biocham --generate-doc
-
-test: biocham_debug
+# slow tests too
+test: biocham_debug jupyter_tests
 	echo "flag(slow_test, _, true), run_tests_and_halt." | ./biocham_debug
 
+jupyter_tests: jupyter
+	PYTHONPATH=$(PWD) jupyter nbconvert --execute --stdout library/examples/cmsb_2017/sigmoids.ipynb > /dev/null
+
 # runs test unit %
 test_%: biocham_debug
 	echo "flag(slow_test, _, true), run_tests_and_halt('$*')." | ./biocham_debug
 
 jupyter: biocham biocham_kernel/commands.js biocham_kernel/commands.py
 	- jupyter kernelspec install --user --name=biocham biocham_kernel
-	- jupyter nbextension install --user biocham_kernel/bc_nb_extensions/menu
-	- jupyter nbextension install --user biocham_kernel/bc_nb_extensions/biocham_gui
-	- cd biocham_kernel/bc_nb_extensions
+	- jupyter nbextension install --user biocham_gui/menu
 	- jupyter nbextension enable --user menu/main
-	- jupyter nbextension enable --user biocham_gui/main
-	- jupyter nbextension uninstall --user gui_toolbar
+	- jupyter nbextension disable biocham_gui/dist/bundle
+	- jupyter nbextension disable biocham_gui/main
+	- jupyter nbextension disable gui_toolbar/main
+
+
 
 biocham_kernel/commands.py: biocham
 	rm -f $@
@@ -135,7 +163,7 @@ web/biocham.zip: biocham-src-$(shell git rev-parse --short HEAD).zip
 	cp $< $@
 
 web: web/biocham.zip web/index.html web/logo.png doc/index.html
-	-rsync -avz $^ lifeware:/nfs/web-epi/biocham4/
+	-rsync -avz $^ doc lifeware:/nfs/web-epi/biocham4/
 	ssh -t lifeware 'sudo chmod -R g+w /nfs/web-epi/biocham4/ && sudo chown -R www-data.lifeware /nfs/web-epi/biocham4/'
 
 cabernet: web
@@ -151,12 +179,3 @@ gadagne: web
 
 gadagne_restart: gadagne
 	ssh -t gadagne 'cd /opt/tmpnb/ && sudo ./cleanup.sh && sudo ./tmpnb_biocham.sh'
-
-release:
-	@read -p "Version number (e.g. 4.1.0): " version && \
-	sed -i'' -e "s/^version('.*')/version('$$version')/" about.pl && \
-	sed -i'' -e "s+^<h1>version.*</h1>+<h1>version $$version $(shell date '+%b %Y')</h1>+" web/index.html
-	@read -p "We will now commit tag and push the new version [press any key]" dummy
-	git commit about.pl web/index.html -m $Version $$version$
-	git tag -a v$$version -m "Version $$version"
-	git push --tags

about.pl

@@ -8,10 +8,10 @@
     about/0
   ]).
 
-version('4.1.0').
+version('4.1.7').
 
 copyright(
-  'Copyright (C) 2003-2017 Inria, EPI Lifeware, Saclay-Île de France, France'
+  'Copyright (C) 2003-2018 Inria, EPI Lifeware, Saclay-Île de France, France'
 ).
 
 license('GNU GPL 2').

biocham_gui/package.json

+{
+  "name": "gui",
+  "version": "1.0.0",
+  "description": "",
+  "main": "src/main.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1",
+    "dev": "webpack --mode development",
+    "build": "webpack --mode production"
+  },
+  "author": "",
+  "license": "ISC",
+  "devDependencies": {
+    "babel-cli": "^6.26.0",
+    "babel-core": "^6.26.0",
+    "babel-loader": "^7.1.4",
+    "babel-plugin-transform-class-properties": "^6.24.1",
+    "babel-plugin-transform-es2015-modules-amd": "^6.24.1",
+    "babel-preset-env": "^1.6.1",
+    "babel-preset-react": "^6.24.1",
+    "css-loader": "^0.28.10",
+    "lodash": "^4.17.5",
+    "react-draggable": "^3.0.5",
+    "style-loader": "^0.20.3",
+    "webpack": "^4.1.1",
+    "webpack-cli": "^2.0.11"
+  },
+  "dependencies": {
+    "phosphor-gridpanel": "^1.0.0-beta.1",
+    "phosphor-widget": "^1.0.0-rc.1",
+    "prop-types": "^15.6.1",
+    "react": "^16.2.0",
+    "react-autocomplete": "^1.8.1",
+    "react-bootstrap": "^0.32.1",
+    "react-burger-menu": "^2.4.2",
+    "react-dock": "^0.2.4",
+    "react-dom": "^16.2.0",
+    "react-grid-layout": "^0.16.6",
+    "react-input-completion": "^1.0.2",
+    "react-resizable": "^1.7.5",
+    "react-tabs": "^2.2.1",
+    "react-transition-group": "^2.3.0",
+    "requirejs": "^2.3.5",
+    "styled-components": "^3.2.3"
+  }
+}

biocham_gui/src/App.js

+import React from 'react';
+import PropTypes from 'prop-types';
+import Menu from './components/menu/Menu'
+import Grid from './components/grid/Grid'
+import Editor from './components/edition/Editor'
+import { menu } from "../../biocham_kernel/cmd_tree"
+
+export default class App extends React.Component {
+    static propTypes = {
+        menu: PropTypes.object.isRequired,
+    }
+
+    static defaultProps = {
+        //the tree.tree object contains all the commands, etc
+        menu: menu
+    }
+
+    initLayout = () => {
+        
+    }
+
+    render() {
+        return (
+            <div style={{width: '100%'}}>
+                <Grid>
+                </Grid>
+            </div>
+        )
+    }
+}

biocham_gui/src/components/Edition/Editor.js

+import React, { Component } from 'react';
+
+export default class Edition extends Component {
+
+    render () {
+        const commands = this.props.items;
+        let commandsInput = (
+            <div>
+                <span className="drag-handle">{this.props.name}</span>
+                <br/>
+                {commands.map((command) => (<label>{command.name} : <input/><br/></label>))}
+            </div>
+        );
+
+        return (
+            <div>
+                {commandsInput}
+            </div>
+        )
+    }
+}

biocham_gui/src/components/grid/Grid.js

+import React, { Component } from 'react';
+import { WidthProvider, Responsive } from 'react-grid-layout';
+import Editor from '../Edition/Editor';
+
+
+const ResponsiveGridLayout = WidthProvider(Responsive);
+
+export default class Grid extends Component {
+    static defaultProps = {
+        className: "layout",
+        cols: { lg: 12, md: 10, sm: 6, xs: 4, xxs: 2 },
+        breakpoints: {lg: 1200, md: 996, sm: 768, xs: 480, xxs: 0},
+        rowHeight: 80,
+        draggableHandle: '.drag-handle',
+        onLayoutChange: function () {},
+    }
+
+
+    state = {
+        layouts: {
+            lg: [
+                {i: 'initial_state', x: 0, y: 0, w: 4, h:5},
+                {i: 'parameters', x: 0, y: 3, w: 4, h:2},
+                {i: 'numerical_simulation', x: 0, y: 6, w: 4, h:2}]
+        },
+        parameters: [],
+        molecules: [],