Add documentations, correct mac and windows problem with logger and t…

README.mkd

@@ -117,6 +117,8 @@ python setup.py install
 
 Requires Python >= 3.11. 
 
+Need to manually install graphviz: `conda install -c conda-forge graphviz`. If not installed and Seed2LP is launched for a graph visualisation of the network, the tool will raise an error and invite the user to install graphviz.
+
 For below requirements, installing Seed2LP will install all needed packages if not already installed.
 
 

networks/toys_communities/communities/com1.txt

@@ -1,2 +1,4 @@
 B1
-B2
+B2
+B3
+B4

seed2lp/_version.py

@@ -1,2 +1,2 @@
-__version_info__ = ('2', '0', '0')
+__version_info__ = ('2', '1', '0')
 __version__ = '.'.join(__version_info__)

seed2lp/argument.py

@@ -624,7 +624,7 @@ def cli_parser() -> argparse.ArgumentParser:
           - guess_check_div: Guess check but also forbids subset of seed as next result in order to reduce intersection of solutions
         """,
         usage="""
-        seed2lp community [community_file_text] [sbml_directory] [result directory] \n 
+        seed2lp community [community_file_text] [sbml_directory] [result_directory] \n 
         """
     )
 

seed2lp/asp/enum-cc.lp

@@ -11,11 +11,11 @@ reaction(R) :- dreaction(R).
 
 
 % the edges are linking reactants to products of each reaction.
-oedge(T,P) :- reactant(T,R) ; product(P,R).
+oedge(T,P) :- reactant(T,_,R,_,_,_) ; product(P,_,R,_,_,_).
 
 % the nodes
-node(M) :- reactant(M,_).
-node(M) :- product(M,_).
+node(M) :- reactant(M,_,_,_,_,_).
+node(M) :- product(M,_,_,_,_,_).
 
 % #show oedge/2.
 % #show node/1.

seed2lp/clingo_lpx.py

@@ -2,11 +2,19 @@
 Clingo lpx functions for launching command and extract results.
 """
 
-import subprocess 
+import subprocess, logging
 import json
-from resource import getrusage, RUSAGE_CHILDREN
+#from resource import getrusage, RUSAGE_CHILDREN
 from .utils import repair_json
-from . import logger, color
+from . import color #logger
+try:
+    from resource import getrusage, RUSAGE_CHILDREN
+except ImportError:
+    RUSAGE_CHILDREN = 0
+    def getrusage(x):
+        class ret:
+            ru_maxrss = 2**20
+        return ret
 
 
 def command(files:list, options:list, nb_model:int=0, time_limit:int=0) -> iter:
@@ -59,15 +67,15 @@ def solve(cmd:list, time_limit:int):
     Returns:
         proc_output (str), err_output (str), error_code (int), memory (float), is_killed (bool)
     """
-
+    logger = logging.getLogger("s2lp")
     cmd.append(f'--outf=2')
     is_killed=False
     try:
         process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
         if time_limit:
             process.wait(timeout=time_limit+60)
     except subprocess.TimeoutExpired:
-        logger.log.error(f'Timeout: {time_limit/60} min expired')
+        logger.error(f'Timeout: {time_limit/60} min expired')
         process.kill()
         process.wait()
         is_killed=True
@@ -78,7 +86,7 @@ def solve(cmd:list, time_limit:int):
     if is_killed:
         error_code=0
     if error_code==1:
-        logger.log.error(f'Timeout: {time_limit/60} min expired')
+        logger.error(f'Timeout: {time_limit/60} min expired')
     return str(proc_output, 'UTF-8'), err_output, error_code, round(memory,3), is_killed
 
 

seed2lp/description.py

@@ -7,7 +7,7 @@
 import re
 from os import path
 from seed2lp.network import Network     
-from . import flux, logger, color
+from . import flux, color # logger,
 import warnings
 import difflib
 import seed2lp.sbml as SBML
@@ -21,15 +21,15 @@
 #defined reactant/4.
 #defined product/4.
 #defined reaction/1.
-link(T,R) :- reactant(T,_,R,_).
-link(R,P) :- product(P,_,R,_).
+link(T,R) :- reactant(T,_,R,_,_,_).
+link(R,P) :- product(P,_,R,_,_,_).
 shape(R,rectangle) :- reaction(R).
 obj_property(edge,arrowhead,vee).
 """
 BISEAU_VIZ_NOREACTION = """
-link(M,P) :- product(P,_,R,_) ; reactant(M,_,R,_).
-link(P,P) :- product(P,_,R,_) ; not reactant(_,_,R,_).
-link(M,M) :- reactant(M,_,R,_), not product(_,_,R,_).
+link(M,P) :- product(P,_,R,_,_,_) ; reactant(M,_,R,_,_,_).
+link(P,P) :- product(P,_,R,_,_,_) ; not reactant(_,_,R,_,_,_).
+link(M,M) :- reactant(M,_,R,_,_,_), not product(_,_,R,_,_,_).
 obj_property(edge,arrowhead,vee).
 """
 
@@ -102,7 +102,7 @@ def get_details(self):
     def details_from_lp(self):
         """Get the network description from lp facts and save it
         """
-        logger.log.info("Start Getting Details from LP file")
+        self.logger.info("Start Getting Details from LP file")
         reactions_composition_df = pd.DataFrame(columns=['reaction', 'metabolite', 'type_metabolite', 'stoichiometry'])
         reaction_df = pd.DataFrame(columns=['reaction', 'low_bound', 'up_bound','is_forward', 'is_reverse', 'is_low_set'])
         only_forward=list()
@@ -251,13 +251,13 @@ def details_from_lp(self):
         #print(reaction_without_reactant)
         #print("REACTION WITHOUT PRODUCT")
         #print(reaction_without_product)
-        save(self.lp_details , full_details)
+        self.save(self.lp_details , full_details)
 
 
     def details_from_cobra(self):
         """Get the network description from sbml file by using cobra and save it
         """
-        logger.log.info("Start Getting Details from Cobra file")
+        self.logger.info("Start Getting Details from Cobra file")
         warnings.filterwarnings("error")
         model = flux.get_model(self.file)
         if not self.keep_import_reactions:
@@ -267,14 +267,14 @@ def details_from_cobra(self):
             full_details += f"{reaction}\t[{reaction.lower_bound}, {reaction.upper_bound}]\n"
 
         self.cobra_details = path.join(self.out_dir, f"{self.name}_{self.short_option}_details_from_cobra.txt")
-        save(self.cobra_details, full_details)
+        self.save(self.cobra_details, full_details)
 
 
     def details_diff(self):
         """Compare the Network description from cobra and lp facts
         save the diff information into file
         """
-        logger.log.info("Start checking diff between Cobra and LP Network")
+        self.logger.info("Start checking diff between Cobra and LP Network")
         diff = ""
         with open(self.cobra_details) as cobra_details:
             cobra_details_text = cobra_details.readlines()
@@ -292,12 +292,13 @@ def details_diff(self):
         lp_details.close()
 
         diff_path = path.join(self.out_dir, f"{self.name}_{self.short_option}_details_diff.txt")
-        save(diff_path, diff)
+        self.save(diff_path, diff)
 
     def render_network(self):
         """From lp facts render the network graph with or without reaction
         """
         import biseau
+        check_graphviz()
         out_file = path.join(self.out_dir, f"{self.name}_{self.short_option}_visu")
 
         print(f"\n\n{color.cyan_dark}############################################")  
@@ -343,10 +344,10 @@ def rewrite_sbml_file(self):
         print(f"############################################\n{color.reset}") 
 
         if self.keep_import_reactions:
-            logger.log.warning("IMPORT REACTION KEPT")
+            self.logger.warning("IMPORT REACTION KEPT")
         else:
-            logger.log.warning("IMPORT REACTION REMOVED BY DEFAULT")
-            logger.log.warning("If you want to keep import reaction\nuse option -kir / --keep-import-reactions")
+            self.logger.warning("IMPORT REACTION REMOVED BY DEFAULT")
+            self.logger.warning("If you want to keep import reaction\nuse option -kir / --keep-import-reactions")
         species=self.name
         original_reactions = SBML.get_listOfReactions(self.model[species])
 
@@ -366,7 +367,7 @@ def rewrite_sbml_file(self):
             if reaction_name in self.deleted_reactions:
                 self.sbml_remove_reaction(reaction, species)
                 rm_reac_message+=f"\n\t- {reaction_name}"
-                logger.log.info(rm_reac_message)
+                self.logger.info(rm_reac_message)
             else:
                 # Change the reversibility
                 is_modif_rev = self.sbml_review_reversibilty(reaction_name, reaction)
@@ -389,11 +390,11 @@ def rewrite_sbml_file(self):
 
         #print and log
         if is_modif_rev_log:
-            logger.log.warning(modif_rev_message)
+            self.logger.warning(modif_rev_message)
         if is_switch_meta_log:
-            logger.log.warning(switch_meta_message)
+            self.logger.warning(switch_meta_message)
         if is_rm_import_log:
-            logger.log.warning(rm_import_message)
+            self.logger.warning(rm_import_message)
 
         # Replace list of parameters because we added new specific parameters for the exchange reactions
         self.sbml_review_parameters(species)
@@ -405,20 +406,30 @@ def rewrite_sbml_file(self):
         file_path = path.join(self.out_dir, self.name+".xml") 
         str_model =  self.sbml_first_line+SBML.etree_to_string(self.sbml[species])
         print(f"File saved at: {file_path}")
-        save(file_path, str_model)
+        self.save(file_path, str_model)
 
-    ######################################################## 
 
+    def save(self, out_file:str, data):
+        """Save file of Network description or graphs
 
-######################## FUNCTIONS ########################
-def save(out_file:str, data):
-    """Save file of Network description or graphs
-
-    Args:
-        out_file (str): Output file path
-        data: Graph or Network details data
-    """
-    with open(out_file, 'w') as f:
-        f.write(data)
-    f.close()
-    logger.log.info(f"File saved at: {out_file}")
+        Args:
+            out_file (str): Output file path
+            data: Graph or Network details data
+        """
+        with open(out_file, 'w') as f:
+            f.write(data)
+        f.close()
+        self.logger.info(f"File saved at: {out_file}")
+
+
+def check_graphviz():
+    import shutil
+    if shutil.which("dot") is None:
+        raise RuntimeError(
+            f"\n\n{color.red_bright}Graphviz is required and missing from your environment.{color.reset}\n"
+            f"First install it with:\n"
+            f"  {color.cyan_dark}conda install -c conda-forge graphviz{color.reset}\n"
+            f"or\n"
+            f"  {color.cyan_dark}sudo apt install graphviz{color.reset}\n"
+            f"Then retry.\n"
+        )

seed2lp/file.py

@@ -1,7 +1,8 @@
+import logging
 from os import path, makedirs, stat, remove
 from json import dump, load
 from csv import writer, reader
-from . import logger
+#from . import logger
 
 
 def existant_path(inpath:str) -> str:
@@ -29,12 +30,13 @@ def is_valid_dir(dirpath):
     Returns:
         bool: True if dir exists, False otherwise
     """
+    logger = logging.getLogger("s2lp")
     if not path.isdir(dirpath):
         try:
             makedirs(dirpath)
             return dirpath
         except OSError as e:
-            logger.log.error(e)
+            logger.error(e)
             return None
     else:
         return dirpath
@@ -64,6 +66,7 @@ def save(filename:str, directory:str, results, type:str, is_result_temp=False):
         type (str): Type of output fils (json or tsv or txt)
     """
 
+    logger = logging.getLogger("s2lp")
     out_file_path = path.join(directory,filename)
     try:
         match type:
@@ -91,7 +94,7 @@ def save(filename:str, directory:str, results, type:str, is_result_temp=False):
                 with open(out_file_path, "w") as f:
                     f.write("\n".join(results))
     except  Exception as e:
-        logger.log.error(f"while saving file: {e}")
+        logger.error(f"while saving file: {e}")