Fix bug in install process.

The *.so are now in the fortran folders, so the MANIFEST.in file was updated
to include those shared objects in the pip source distribution

Makefile

@@ -15,7 +15,7 @@ endif
 .PHONY: clean version selfex venv doc
 
 
-selfex: clean
+selfex: results purge
 	@echo "Creating the self-extractible setup program... "
 #	update the version
 	@cp ./src/msspec/version.py ./src/msspec/version.py.bak
@@ -58,6 +58,13 @@ clean:
 	@+$(MAKE) -C doc/ clean $(SUPPRESS_OUPUT)
 	@rm -rf package
 
+purge: clean
+	@echo "Removing also shared objects..."
+	@find ./src -type f -name '*.so' -exec rm -f {} +
+
+results:
+	@+$(MAKE) -C src results
+
 
 venv:
 	@virtualenv --python=python3 --system-site-packages ci_venv $(SUPPRESS_OUPUT)

README.md

@@ -5,11 +5,107 @@ This is the Python MsSpec version with support for Python 3.x and dynamic memory
 
 
 
-To install
-==========
+To work with the git repository
+===============================
+
+It is higly recommended to work in a Python virtual environment.
+To create one, you can use:
 
 
 ```Bash
-make selfex
-./pymsspec-###.setup
+virtualenv --python=python3 msspec_venv
 ```
+
+or 
+
+```Bash
+virtualenv --python=python3 --system-site-packages msspec_venv
+```
+
+to activate the virtual environment (if you are in the folder where you created "msspec\_venv"):
+
+```Bash
+source ./msspec_venv/bin/activate
+```
+
+To get the python package dependencies, you can install the requirements with the provided requirements.txt file.
+
+```Bash
+pip install --upgrade -r requirements.txt
+```
+
+You also need to export the path to the msspec package in the PYTHONPATH variable (replace the whereisthegitrepo part
+of the string with the actual absolute path of your repo.
+
+```Bash
+export PYTHONPATH=/whereisthegitrepo/src:$PYTHONPATH
+```
+
+Finally you need to compile the fortran libs:
+
+```Bash
+make pybinding
+```
+
+That's all. All you need to do each time you want to work with msspec is:
+
+- To activate the virtual environment
+- Export the path to msspec package in the PYTHONPATH variable
+
+
+
+To create a self-extracible archive
+===================================
+
+If you want to create a setup program to install msspec:
+
+At the root of the repo, type in
+
+```Bash
+make selfex
+```
+
+This will compile the code and create the results of unit tests, then it will create a self-extractible archive in the package folder
+
+
+To install the \*.setup file
+============================
+
+Just execute the file with a shell
+
+```Bash
+sh ./MsSpec-###.setup
+```
+
+Replace ### with the version number.
+
+To automatically accept the defaults you could type in
+
+```Bash
+sh ./MsSpec-###.setup --accept -- -y
+```
+
+and to make the install process verbose:
+
+```Bash
+sh ./MsSpec-###.setup -- -d
+```
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

requirements.txt

@@ -0,0 +1,9 @@
+numpy
+ase
+h5py
+lxml
+pint
+terminaltables
+pycairo
+coverage
+sphinx

src/MANIFEST.in

@@ -1,3 +1,3 @@
-include msspec/spec/*.so
-include msspec/phagen/*.so
+include msspec/spec/fortran/*.so
+include msspec/phagen/fortran/*.so
 include msspec/results.txt

src/Makefile

@@ -21,7 +21,9 @@ pybinding:
 	@+$(MAKE) -C msspec/spec/fortran pybinding $(SUPPRESS_OUPUT)
 	@+$(MAKE) -C msspec/phagen/fortran pybinding $(SUPPRESS_OUPUT)
 
-results: pybinding
+results: msspec/results.txt
+
+msspec/results.txt: pybinding
 	@echo "Generating results for unittests"
 	@coverage run --source=./ --omit=msspec/es/*,msspec/msspecgui/* msspec/create_tests_results.py 1>/dev/null
 #	create the html coverage report

src/msspec/spec/fortran/Makefile

@@ -39,6 +39,8 @@ objects_src += $(renormalization_src) $(phd_se_noso_nosp_nosym_src)
 objects_src += $(eig_common_src) $(eig_mi_src) $(eig_pw_src)
 objects:=$(patsubst %.f,%.o, $(objects_src))
 
+libs_targets := phd_se_noso_nosp_nosym.target eig_mi.target eig_pw.target
+
 EXE=prog
 
 ifeq ($(DEBUG),1)
@@ -53,22 +55,22 @@ export COMP_OPTS
 .PHONY: clean
 
 
-pybinding: phd_se_noso_nosp_nosym eig_mi eig_pw
+pybinding: $(libs_targets)
 
-phd_se_noso_nosp_nosym: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(phd_se_noso_nosp_nosym_obj)
+phd_se_noso_nosp_nosym.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(phd_se_noso_nosp_nosym_obj)
 	@echo "building Python binding..."      
-	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $@ phd_se_noso_nosp_nosym/main.f
-#	@cp $@.cpython*.so ../
+	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) phd_se_noso_nosp_nosym/main.f
+	@touch $@
 
-eig_mi: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_mi_obj)
+eig_mi.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_mi_obj)
 	@echo "building Python binding..."      
-	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $@ eig/mi/main.f
-#	@cp $@.cpython*.so ../
+	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/mi/main.f
+	@touch $@
 
-eig_pw: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_pw_obj)
+eig_pw.target: $(memalloc_obj) $(cluster_gen_obj) $(common_sub_obj) $(renormalization_obj) $(eig_common_obj) $(eig_pw_obj)
 	@echo "building Python binding..."      
-	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $@ eig/pw/main.f
-#	@cp $@.cpython*.so ../
+	@$(F2PY) $(includes) $^ $(F2PY_OPTS) -c -m $(patsubst %.target, %, $@) eig/pw/main.f
+	@touch $@
 
 %.o: %.f
 	@echo "compiling $@..."
@@ -78,3 +80,4 @@ clean:
 	@echo "cleaning..."                                               
 	@rm -rf *.o *.mod
 	@rm -rf $(objects)
+	@rm -rf $(libs_targets)