From 1db975233a0e580bf9fe20a824df0727b93d43de Mon Sep 17 00:00:00 2001
From: sylvain tricot <stricot@mr084122.spm.univ-rennes1.fr>
Date: Wed, 13 Jan 2021 18:26:08 +0100
Subject: [PATCH 1/6] Small changes to Makefiles.

---
 Makefile       | 4 ++++
 src/Makefile   | 2 +-
 src/options.mk | 3 +++
 3 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index aabbbd9..0440e6b 100644
--- a/Makefile
+++ b/Makefile
@@ -52,3 +52,7 @@ doc:
 clean::
 	@+$(MAKE) -C src/ clean
 
+
+help:
+	@echo "Top Makefile help message"
+
diff --git a/src/Makefile b/src/Makefile
index d2dda44..3b2f40b 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -56,5 +56,5 @@ clean::
 
 
 help:
-	@echo "help message"
+	@echo "SRC Makefile help message"
 
diff --git a/src/options.mk b/src/options.mk
index 6e432dd..bec887b 100644
--- a/src/options.mk
+++ b/src/options.mk
@@ -69,6 +69,9 @@ OBJS = $(addprefix $(BUILDDIR)/, $(patsubst %.f,%.o, $(filter-out $(MAIN_F), $(S
 
 .PHONY: clean obj all info
 
+help:
+
+
 info:
 	@echo "Compilation information for msspec $(VERSION)"
 	@echo "FC    : $(FC)"

From 72ba908be1eb9e2158611d7600b19dde9ec7f75f Mon Sep 17 00:00:00 2001
From: sylvain tricot <stricot@mr084122.spm.univ-rennes1.fr>
Date: Thu, 21 Jan 2021 11:12:24 +0100
Subject: [PATCH 2/6] Improve python path and version checking.

In the top Makefile, the Python path and version are first checked
before going any further. This is now done in a more cleaner way
by looking at the "sys.version_info variable"
---
 Makefile | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/Makefile b/Makefile
index 0440e6b..7767837 100644
--- a/Makefile
+++ b/Makefile
@@ -1,19 +1,18 @@
 include src/options.mk
 
 PYTHON = python
+PYMAJ  = 3
+PYMIN  = 6
 
-# Checking Python version
+# Checking Python path and version
 PYTHON_EXE := $(shell command -v $(PYTHON) 2> /dev/null)
 
 ifndef PYTHON_EXE
   $(error Unable to find the $(PYTHON) executable!)
 endif
 
-PYTHON_VERSION_MAJOR := $(shell $(PYTHON_EXE) --version 2>&1 | cut -d" " -f2 | cut -d. -f1)
-PYTHON_VERSION_MINOR := $(shell $(PYTHON_EXE) --version 2>&1 | cut -d" " -f2 | cut -d. -f2)
-
-ifneq ($(shell test $(PYTHON_VERSION_MAJOR) -ge 3 -a $(PYTHON_VERSION_MINOR) -ge 6; echo $$?),0)
-  $(error Python version >= 3.6 is needed!)
+ifeq ($(shell python -c "import sys; exit(sys.version_info >= ($(PYMAJ),$(PYMIN)))"; echo $$?),0)
+   $(error Python version >= $(PYMAJ).$(PYMIN) is needed!)
 endif
 
 

From 527ad80b036ffa78c9ff770503b57111bd22e51e Mon Sep 17 00:00:00 2001
From: sylvain tricot <sylvain.tricot@.univ-rennes1.fr>
Date: Thu, 21 Jan 2021 13:51:39 +0100
Subject: [PATCH 3/6] Simplify pip.freeze requirements file.

---
 src/pip.freeze | 49 +++----------------------------------------------
 1 file changed, 3 insertions(+), 46 deletions(-)

diff --git a/src/pip.freeze b/src/pip.freeze
index 49e5fc2..0a7d654 100644
--- a/src/pip.freeze
+++ b/src/pip.freeze
@@ -1,57 +1,14 @@
-alabaster==0.7.12
 ase==3.19.1
-Babel==2.8.0
-backcall==0.1.0
-certifi==2020.4.5.1
-chardet==3.0.4
-coverage==5.1
-cycler==0.10.0
-decorator==4.4.2
-docutils==0.16
 h5py==2.10.0
-idna==2.9
-imagesize==1.2.0
 ipython==7.13.0
-ipython-genutils==0.2.0
-jedi==0.17.0
-Jinja2==2.11.2
 lxml==4.5.0
-MarkupSafe==1.1.1
 matplotlib==2.1.1
 numpy==1.18.2
-packaging==20.3
-parso==0.7.0
-pex==2.1.11
-pexpect==4.8.0
-pickleshare==0.7.5
-Pillow==7.1.1
 Pint==0.11
-pip==20.0.2
-prompt-toolkit==3.0.5
-ptyprocess==0.6.0
+#pip==20.0.2
 pycairo==1.19.1
-Pygments==2.6.1
-pyparsing==2.4.7
-python-dateutil==2.8.1
-pytz==2019.3
-requests==2.23.0
 scipy==1.4.1
-scons==3.1.2
-setuptools==46.1.3
 setuptools-scm==3.5.0
-six==1.14.0
-snowballstemmer==2.0.0
-spglib==1.14.1.post0
-Sphinx==3.0.1
-sphinxcontrib-applehelp==1.0.2
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==1.0.3
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.4
 terminaltables==3.1.0
-traitlets==4.3.3
-urllib3==1.25.8
-wcwidth==0.1.9
-wheel==0.34.2
-#wxPython@https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-18.04/wxPython-4.0.7.post2-cp36-cp36m-linux_x86_64.whl
+#wxPython@https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-10/wxPython-4.1.0-cp37-cp37m-linux_x86_64.whl
+#wxPython@https://extras.wxpython.org/wxPython4/extras/linux/gtk3/debian-9/wxPython-4.0.7.post2-cp35-cp35m-linux_x86_64.whl

From d7f004ebec76c52ff501c315d2dba8d819e24e05 Mon Sep 17 00:00:00 2001
From: sylvain tricot <sylvain.tricot@.univ-rennes1.fr>
Date: Fri, 22 Jan 2021 17:03:53 +0100
Subject: [PATCH 4/6] Changes on Makefile to be compatible with Docker.

---
 Makefile               | 19 ++++++++++---------
 src/Makefile           |  4 +++-
 src/msspec.sh.template |  2 +-
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/Makefile b/Makefile
index 7767837..b96333b 100644
--- a/Makefile
+++ b/Makefile
@@ -11,7 +11,7 @@ ifndef PYTHON_EXE
   $(error Unable to find the $(PYTHON) executable!)
 endif
 
-ifeq ($(shell python -c "import sys; exit(sys.version_info >= ($(PYMAJ),$(PYMIN)))"; echo $$?),0)
+ifeq ($(shell $(PYTHON_EXE) -c "import sys; exit(sys.version_info >= ($(PYMAJ),$(PYMIN)))"; echo $$?),0)
    $(error Python version >= $(PYMAJ).$(PYMIN) is needed!)
 endif
 
@@ -19,19 +19,20 @@ endif
 .PHONY: pybinding install devel venv doc clean
 
 
-pybinding:
-	@+$(MAKE) -C src pybinding
+pybinding: venv
+	@+. $(VENV_PATH)/bin/activate && $(MAKE) -C src pybinding
 
 
 venv:
-	virtualenv --python=$(PYTHON_EXE) --prompt="(msspec-$(VERSION)) " $(VENV_PATH)
-	. $(VENV_PATH)/bin/activate && pip install --upgrade pip && pip install -r src/pip.freeze
+	@virtualenv --python=$(PYTHON_EXE) --prompt="(msspec-$(VERSION)) " $(VENV_PATH)
+	@. $(VENV_PATH)/bin/activate && pip install --upgrade pip && pip install -r src/pip.freeze
 
 
-install: pybinding venv
-	@+$(MAKE) -C src sdist
-	@+$(MAKE) -C src frontend
-	@. $(VENV_PATH)/bin/activate && pip install src/dist/msspec-$(VERSION).tar.gz
+install: pybinding
+	@+. $(VENV_PATH)/bin/activate && $(MAKE) -C src sdist
+	@+. $(VENV_PATH)/bin/activate && $(MAKE) -C src frontend
+	@+. $(VENV_PATH)/bin/activate && pip install src/dist/msspec-$(VERSION).tar.gz
+	@echo "Do not forget to check that $(INSTALL_PREFIX)/bin is set in your \$$PATH"
 
 
 devel: VENV_PATH = ./_venv
diff --git a/src/Makefile b/src/Makefile
index 3b2f40b..1e727c8 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -16,7 +16,9 @@ dist/msspec-$(VERSION).tar.gz: VERSION
 
 $(INSTALL_PREFIX)/bin/msspec: msspec.sh.template VERSION
 	@echo "Installing frontend command..."
-	@cat $< | sed 's/__VERSION__/$(VERSION)/' > $@
+	@mkdir -p $(dir $@)
+	@cat $< | sed -e 's/__VERSION__/$(VERSION)/' -e 's#__VENV_PATH__#$(VENV_PATH)#' > $@
+	#@cat $< | sed 's/__VERSION__/$(VERSION)/' > $@
 	@chmod u+x $@
 
 
diff --git a/src/msspec.sh.template b/src/msspec.sh.template
index b6cc2ea..22ef574 100644
--- a/src/msspec.sh.template
+++ b/src/msspec.sh.template
@@ -3,7 +3,7 @@
 SCRIPT_PATH="$0"
 SCRIPT_NAME=$(basename "$SCRIPT_PATH")
 VERSION="__VERSION__"
-VENV_PATH="$HOME/.local/src/msspec_venv_$VERSION"
+VENV_PATH="__VENV_PATH__"
 
 # Check venv path
 if ! [ -d "$VENV_PATH" ]; then

From da92ce048f43eb42bab0c2120f7dcffb53a894bd Mon Sep 17 00:00:00 2001
From: sylvain tricot <sylvain.tricot@.univ-rennes1.fr>
Date: Fri, 22 Jan 2021 17:31:46 +0100
Subject: [PATCH 5/6] Fix file permissions in frontend install target.

---
 src/Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/Makefile b/src/Makefile
index 1e727c8..189f6c6 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -19,7 +19,7 @@ $(INSTALL_PREFIX)/bin/msspec: msspec.sh.template VERSION
 	@mkdir -p $(dir $@)
 	@cat $< | sed -e 's/__VERSION__/$(VERSION)/' -e 's#__VENV_PATH__#$(VENV_PATH)#' > $@
 	#@cat $< | sed 's/__VERSION__/$(VERSION)/' > $@
-	@chmod u+x $@
+	@chmod 755 $@
 
 
 pybinding:

From 7921f813c42eb819f1acaabbf155feb4f7a9e12e Mon Sep 17 00:00:00 2001
From: sylvain tricot <sylvain.tricot@.univ-rennes1.fr>
Date: Fri, 22 Jan 2021 17:32:12 +0100
Subject: [PATCH 6/6] Add a Dockerfile.

---
 Dockerfile | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..4b8b8f2
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,30 @@
+# Get the base Python image
+FROM python:3.7
+
+# Set the working directory in the container
+RUN useradd -ms /bin/bash msspec
+WORKDIR /code
+
+# Fetch the code
+COPY fresh .
+
+ENV LANG=en_US.UTF-8
+ENV PATH=/opt/bin:$PATH
+
+# Install system dependencies
+RUN apt-get update && \
+    apt-get install -y virtualenv gfortran locales python3-wxgtk4.0
+
+# Reconfigure the locales
+RUN sed -i -e "s/# $LANG.*/$LANG UTF-8/" /etc/locale.gen && \
+    dpkg-reconfigure --frontend=noninteractive locales && \
+    update-locale LANG=$LANG
+    
+# Install msspec
+RUN make install VERBOSE=1 INSTALL_PREFIX=/opt
+
+#RUN echo "/usr/lib/python3/dist-packages" > /opt/src/msspec_venv_*/lib/python3.7/site-packages/system_packages.pth
+
+USER msspec
+
+ENTRYPOINT ["msspec"]