added tests and updated version info parser

binarycpython.yml

-# /user/HS128/dh00601/.config/tmuxinator/binaryc.yml
-
-name: binarycpython
-root: <%= ENV["BINARYC_PYTHON"] %>
-
-
-windows:
-  - binarycpython:
-      layout: tiled
-      panes:
-        - ls
-        - subl .
-        - cd $BINARYC_DIR/
-        - cd $BINARYC_DATA_ROOT/
\ No newline at end of file

binarycpython/utils/functions.py

@@ -155,90 +155,163 @@ def parse_binary_c_version_info(version_info_string):
 
     version_info_dict = {}
 
-    for line in version_info_string.splitlines():
-        line = line.strip()
-        if line == "":
-            continue
-        if " is " in line:
-            split = line.split(" is ")
-            version_info_dict[split[0].strip()] = split[1].strip()
-        else:
-            if line.startswith("Binary_c/nucsyn"):
-                version_info_dict["intro"] = line
-            elif line.startswith("Email"):
-                emails = line.split("Email ")[1].split(",")
-                cleaned_emails = [email.strip() for email in emails]
-                version_info_dict["emails"] = cleaned_emails
-            elif line.startswith("DTlimit"):
-                split = line.split(" : ")
-                version_info_dict[split[0]] = ": ".join(split[1:])
-            elif line.startswith("Version"):
-                split = line.split("Version ")
-                version_number = split[1]
-                version_info_dict["version_number"] = version_number
-            elif line.startswith("git URL"):
-                split = line.split("git URL ")
-                git_url = split[1]
-                version_info_dict["git_url"] = git_url
-            elif line.startswith("Build: "):
-                split = line.split("Build: ")
-                build = split[1]
-                version_info_dict["build"] = build
-            elif line.startswith("Compiled for "):
-                split = line.split("Compiled for ")
-                compiled_for = split[1]
-                version_info_dict["compiled_for"] = compiled_for
-            elif line.startswith("Stack limit "):
-                split = line.split("Stack limit ")
-                stack_limit = split[1]
-                version_info_dict["stack_limit"] = stack_limit
-            elif line.startswith("SVN URL "):
-                split = line.split("SVN URL ")
-                svn_url = split[1]
-                version_info_dict["svn_url"] = svn_url
-            elif line.startswith("git branch "):
-                split = line.split("git branch ")
-                git_branch = split[1]
-                version_info_dict["git_branch"] = git_branch
-            elif line.startswith("_SC_CLK_TCK"):
-                split = line.split(" = ")
-                _SC_CLK_TCK = split[1]
-                version_info_dict["_SC_CLK_TCK"] = _SC_CLK_TCK
-            elif line.startswith("Random number mean "):
-                split = line.split("Random number mean ")
-                random_number_mean = split[1]
-                version_info_dict["Random number mean"] = random_number_mean
-            elif line.startswith("SVN revision "):
-                split = line.split("SVN revision ")
-                svn_revision = split[1]
-                version_info_dict["svn_revision"] = svn_revision
-            elif line.startswith("Size of :"):
-                split = line.split("Size of :")
-                data_type_sizes = split[1]
-                version_info_dict["data_type_sizes"] = data_type_sizes
-            elif line.startswith("git revision "):
-                split = line.split("git revision ")
-                git_revision = split[1]
-                version_info_dict["git_revision"] = git_revision
-            elif line.startswith("BINARY_C_PRE_VERSION "):
-                split = line.split("BINARY_C_PRE_VERSION ")
-                binary_c_pre_version = split[1]
-                version_info_dict["binary_c_pre_version"] = binary_c_pre_version
-            elif line.startswith("Comenv accretion:"):
-                split = line.split("Comenv accretion:")
-                comenv_accretion = split[1]
-                version_info_dict["comenv_accretion"] = comenv_accretion
-            elif line.startswith("Compiled in parameters:"):
-                split = line.split("Compiled in parameters:")
-                compiled_in_parameters = split[1]
-                version_info_dict["compiled_in_parameters"] = compiled_in_parameters
-            elif line.startswith("__short__ is"):
-                split = line.split("__short__ is")
-                short_type = split[1]
-                version_info_dict["short_type"] = short_type
-            else:
-                print("Still found unmatched items!:\n{}".format(repr(line)))
+    # Clean data and put in correct shape
+    splitted = version_info_string.strip().splitlines()
+    cleaned = set([el.strip() for el in splitted if not el == ""])
+
+    ##########################
+    # Isotopes:
+    # Split off
+    isotopes = set([el for el in cleaned if el.startswith('Isotope ')])
+    cleaned = cleaned - isotopes
+
+    isotope_dict = {}
+    for el in isotopes:
+        split_info = el.split("Isotope ")[-1].strip().split(" is ")
+
+        isotope_info = split_info[-1]
+        name = isotope_info.split(' ')[0].strip()
+
+        # Get details
+        mass_g = float(isotope_info.split(",")[0].split('(')[1].split("=")[-1][:-2].strip())
+        mass_amu = float(isotope_info.split(",")[0].split('(')[-1].split("=")[-1].strip())
+        mass_mev = float(isotope_info.split(",")[-3].split("=")[-1].replace(")", "").strip())
+        A = int(isotope_info.split(",")[-1].strip().split("=")[-1].replace(")", ""))
+        Z = int(isotope_info.split(",")[-2].strip().split("=")[-1])
+
+        #
+        isotope_dict[int(split_info[0])] = {'name': name, 'Z': Z, 'A': A, 'mass_mev': mass_mev, 'mass_g': mass_g, 'mass_amu': mass_amu}
+    version_info_dict['isotopes'] = isotope_dict
+
+    ##########################
+    # Argpairs:
+    # Split off
+    argpairs = set([el for el in cleaned if el.startswith('ArgPair')])
+    cleaned = cleaned - argpairs
 
+    argpair_dict = {}
+    for el in sorted(argpairs):
+        split_info = el.split("ArgPair ")[-1].split(" ")
+
+        if not argpair_dict.get(split_info[0], None):
+            argpair_dict[split_info[0]] = {split_info[1]: split_info[2]}
+        else:
+            argpair_dict[split_info[0]][split_info[1]] = split_info[2]
+
+    version_info_dict['argpairs'] = argpair_dict
+
+    ##########################
+    # ensembles:
+    # Split off
+    ensembles = set([el for el in cleaned if el.startswith('Ensemble')])
+    cleaned = cleaned - ensembles
+
+    ensemble_dict = {}
+    for el in ensembles:
+        split_info = el.split("Ensemble ")[-1].split(" is ")
+        if len(split_info)>1:
+            ensemble_dict[int(split_info[0])] = split_info[-1]
+    version_info_dict['ensembles'] = ensemble_dict
+
+    ##########################
+    # macros:
+    # Split off
+    macros = set([el for el in cleaned if el.startswith('macroxyz')])
+    cleaned = cleaned - macros
+
+    param_type_dict = {
+        'STRING': str,
+        'FLOAT': float,
+        'MACRO': str,
+        'INT': int,
+        'LONG_INT': int,
+    }
+
+    macros_dict = {}
+    for el in macros:
+        split_info = el.split("macroxyz ")[-1].split(" : ")
+        param_type = split_info[0]
+
+        new_split = "".join(split_info[1:]).split(" is ")
+        param_name = new_split[0]
+        param_value = " is ".join(new_split[1:])
+        # Sometimes the macros have extra information behind it. Needs an update in outputting by binary_c
+        try:
+            macros_dict[param_name] = param_type_dict[param_type](param_value)
+        except ValueError:
+            macros_dict[param_name] = str(param_value)
+    version_info_dict['macros'] = macros_dict
+
+    ##########################
+    # Elements:
+    # Split off:
+    elements = set([el for el in cleaned if el.startswith('Element')])
+    cleaned = cleaned - elements
+
+    # Fill dict:
+    elements_dict = {}
+    for el in elements:
+        split_info = el.split("Element ")[-1].split(" : ")
+        name_info = split_info[0].split(" is ")
+
+        # get isotope info
+        isotopes = {}
+        if not split_info[-1][0]=='0':
+            isotope_string = split_info[-1].split(" = ")[-1]
+            isotopes = {int(split_isotope.split("=")[0]):split_isotope.split("=")[1] for split_isotope in isotope_string.split(" ")}
+
+        elements_dict[int(name_info[0])] = {'name': name_info[-1], 'atomic_number': int(name_info[0]), 'amt_isotopes': len(isotopes), 'isotopes': isotopes}
+    version_info_dict['elements'] = version_info_dict
+
+    ##########################
+    # dt_limits:
+    # split off
+    dt_limits = set([el for el in cleaned if el.startswith('DTlimit')])
+    cleaned = cleaned - dt_limits
+
+    # Fill dict
+    dt_limits_dict = {}
+    for el in dt_limits:
+        split_info = el.split("DTlimit ")[-1].split(" : ")
+        dt_limits_dict[split_info[1].strip()] = {'index': int(split_info[0]), 'value': float(split_info[-1])}
+
+    version_info_dict['dt_limits'] = dt_limits_dict
+
+    ##########################
+    # Nucleosynthesis sources:
+    # Split off
+    nucsyn_sources = set([el for el in cleaned if el.startswith('Nucleosynthesis')])
+    cleaned = cleaned - nucsyn_sources
+
+    # Fill dict
+    nucsyn_sources_dict = {}
+    for el in nucsyn_sources:
+        split_info = el.split("Nucleosynthesis source")[-1].strip().split(" is ")
+        nucsyn_sources_dict[int(split_info[0])] = split_info[-1]
+
+    version_info_dict['nucleosynthesis_sources'] = nucsyn_sources_dict
+
+    ##########################
+    # miscellaneous:
+    # All those that I didnt catch with the above filters. Could try to get some more out though.
+    # TODO: filter a bit more.
+
+    misc_dict = {}
+    git_revision = [el for el in cleaned if el.startswith('git revision')]
+    misc_dict['git_revision'] = git_revision[0].split("git revision ")[-1].replace("\"", '')
+
+    git_branch = [el for el in cleaned if el.startswith('git branch')]
+    misc_dict['git_branch'] = git_branch[0].split("git branch ")[-1].replace("\"", '')
+
+    build = [el for el in cleaned if el.startswith('Build')]
+    misc_dict['build'] = build[0].split("Build: ")[-1].replace("\"", '')
+
+    email = [el for el in cleaned if el.startswith('Email')]
+    misc_dict['email'] = email[0].split("Email ")[-1].split(',')
+
+    misc_dict['uncaught'] = cleaned
+
+    version_info_dict['miscellaneous'] = misc_dict
     return version_info_dict
 
 
@@ -727,7 +800,9 @@ def inspect_dict(dict_1, indent=0, print_structure=True):
         if print_structure:
             print("\t" * indent, key, type(value))
         if isinstance(value, dict):
-            structure_dict[key] = inspect_dict(value, indent=indent + 1, print_structure=print_structure)
+            structure_dict[key] = inspect_dict(
+                value, indent=indent + 1, print_structure=print_structure
+            )
     return structure_dict
 
 

binarycpython/utils/grid_options_defaults.py

@@ -17,7 +17,6 @@ grid_options_defaults_dict = {
     "main_pid": -1,  # Placeholder for the main process id of the run.
     # "output_dir":
     "commandline_input": "",
-
     ##########################
     # Execution log:
     ##########################
@@ -73,7 +72,7 @@ grid_options_defaults_dict = {
         "grid",
         "source_file",
     ],  # Available choices for type of population generation # TODO: fill later with monte carlo etc
-    "source_file_filename": None, # filename for the source
+    "source_file_filename": None,  # filename for the source
     "count": 0,  # total count of systems
     "probtot": 0,  # total probability
     "weight": 1.0,  # weighting for the probability
@@ -121,46 +120,43 @@ grid_options_defaults_dict = {
     # Slurm stuff
     ########################################
     "slurm": 0,  # dont use the slurm by default. 1 = use slurm
-    "slurm_ntasks": 1, # CPUs required per array job: usually only need this
+    "slurm_ntasks": 1,  # CPUs required per array job: usually only need this
     "slurm_command": "",  # Command that slurm runs (e.g. evolve or join_datafiles)
     "slurm_dir": "",  # working directory containing scripts output logs etc.
-    "slurm_njobs": 0, # number of scripts; set to 0 as default
-    "slurm_jobid": '', # slurm job id (%A)
-    "slurm_memory": 512, # in MB, the memory use of the job
-    "slurm_warn_max_memory": 1024, # in MB : warn if mem req. > this
-    "slurm_use_all_node_CPUs": 0, # 1 = use all of a node's CPUs. 0 = use a given amount of CPUs
-    "slurm_postpone_join": 0, # if 1 do not join on slurm, join elsewhere. want to do it off the slurm grid (e.g. with more RAM)
-    "slurm_jobarrayindex": '', # slurm job array index (%a)
-    "slurm_jobname": 'binary_grid', # default
+    "slurm_njobs": 0,  # number of scripts; set to 0 as default
+    "slurm_jobid": "",  # slurm job id (%A)
+    "slurm_memory": 512,  # in MB, the memory use of the job
+    "slurm_warn_max_memory": 1024,  # in MB : warn if mem req. > this
+    "slurm_use_all_node_CPUs": 0,  # 1 = use all of a node's CPUs. 0 = use a given amount of CPUs
+    "slurm_postpone_join": 0,  # if 1 do not join on slurm, join elsewhere. want to do it off the slurm grid (e.g. with more RAM)
+    "slurm_jobarrayindex": "",  # slurm job array index (%a)
+    "slurm_jobname": "binary_grid",  # default
     "slurm_partition": None,
-    "slurm_time": 0, # total time. 0 = infinite time
-    "slurm_postpone_sbatch": 0, # if 1: don't submit, just make the script
-    "slurm_array": None,# override for --array, useful for rerunning jobs
-    "slurm_use_all_node_CPUs": 0, # if given nodes, set to 1
-                                # if given CPUs, set to 0
+    "slurm_time": 0,  # total time. 0 = infinite time
+    "slurm_postpone_sbatch": 0,  # if 1: don't submit, just make the script
+    "slurm_array": None,  # override for --array, useful for rerunning jobs
+    "slurm_use_all_node_CPUs": 0,  # if given nodes, set to 1
+    # if given CPUs, set to 0
     # you will want to use this if your Slurm SelectType is e.g. linear
     # which means it allocates all the CPUs in a node to the job
-    "slurm_control_CPUs": 0, # if so, leave this many for Pythons control (0)
-    "slurm_array": None, # override for --array, useful for rerunning jobs
-    "slurm_partition": None, # MUST be defined
-    "slurm_extra_settings": {}, # Place to put extra configuration for the SLURM batch file. The key and value of the dict will become the key and value of the line in te slurm batch file. Will be put in after all the other settings (and before the command). Take care not to overwrite something without really meaning to do so. 
-
-
+    "slurm_control_CPUs": 0,  # if so, leave this many for Pythons control (0)
+    "slurm_array": None,  # override for --array, useful for rerunning jobs
+    "slurm_partition": None,  # MUST be defined
+    "slurm_extra_settings": {},  # Place to put extra configuration for the SLURM batch file. The key and value of the dict will become the key and value of the line in te slurm batch file. Will be put in after all the other settings (and before the command). Take care not to overwrite something without really meaning to do so.
     ########################################
     # Condor stuff
     ########################################
-    "condor": 0, # 1 to use condor, 0 otherwise
-    "condor_command": '', # condor command e.g. "evolve", "join"
-    "condor_dir": '', # working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all)
-    "condor_njobs": '', # number of scripts/jobs that CONDOR will run in total
-    "condor_jobid": '', # condor job id
-    "condor_postpone_join": 0, # if 1, data is not joined, e.g. if you want to do it off the condor grid (e.g. with more RAM)
+    "condor": 0,  # 1 to use condor, 0 otherwise
+    "condor_command": "",  # condor command e.g. "evolve", "join"
+    "condor_dir": "",  # working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all)
+    "condor_njobs": "",  # number of scripts/jobs that CONDOR will run in total
+    "condor_jobid": "",  # condor job id
+    "condor_postpone_join": 0,  # if 1, data is not joined, e.g. if you want to do it off the condor grid (e.g. with more RAM)
     # "condor_join_machine": None, # if defined then this is the machine on which the join command should be launched (must be sshable and not postponed)
-    "condor_join_pwd": '', # directory the join should be in (defaults to $ENV{PWD} if undef)
-    "condor_memory": 1024, # in MB, the memory use (ImageSize) of the job
-    "condor_universe": 'vanilla', # usually vanilla universe
-    "condor_extra_settings": {}, # Place to put extra configuration for the CONDOR submit file. The key and value of the dict will become the key and value of the line in te slurm batch file. Will be put in after all the other settings (and before the command). Take care not to overwrite something without really meaning to do so. 
-
+    "condor_join_pwd": "",  # directory the join should be in (defaults to $ENV{PWD} if undef)
+    "condor_memory": 1024,  # in MB, the memory use (ImageSize) of the job
+    "condor_universe": "vanilla",  # usually vanilla universe
+    "condor_extra_settings": {},  # Place to put extra configuration for the CONDOR submit file. The key and value of the dict will become the key and value of the line in te slurm batch file. Will be put in after all the other settings (and before the command). Take care not to overwrite something without really meaning to do so.
     # snapshots and checkpoints
     # condor_snapshot_on_kill=>0, # if 1 snapshot on SIGKILL before exit
     # condor_load_from_snapshot=>0, # if 1 check for snapshot .sv file and load it if found
@@ -180,7 +176,6 @@ grid_options_defaults_dict = {
     # condor_resubmit_submitted=>0,
     # condor_resubmit_running=>0,
     # condor_resubmit_crashed=>0,
-
     ##########################
     # Unordered. Need to go through this. Copied from the perl implementation.
     ##########################

binarycpython/utils/hpc_functions.py

@@ -12,6 +12,7 @@ import time
 import subprocess
 import __main__ as main
 
+
 def get_slurm_version():
     """
     Function that checks whether slurm is installed and returns the version if its installed.
@@ -23,7 +24,7 @@ def get_slurm_version():
 
     try:
         slurm_version = (
-            subprocess.run(['sinfo', "-V"], stdout=subprocess.PIPE, check=True)
+            subprocess.run(["sinfo", "-V"], stdout=subprocess.PIPE, check=True)
             .stdout.decode("utf-8")
             .split()
         )[1]
@@ -38,6 +39,7 @@ def get_slurm_version():
 
     return slurm_version
 
+
 def get_condor_version():
     """
     Function that checks whether slurm is installed and returns the version if its installed.
@@ -51,7 +53,9 @@ def get_condor_version():
 
     try:
         condor_version = (
-            subprocess.run(['condor_q', "--version"], stdout=subprocess.PIPE, check=True)
+            subprocess.run(
+                ["condor_q", "--version"], stdout=subprocess.PIPE, check=True
+            )
             .stdout.decode("utf-8")
             .split()
         )[1]
@@ -66,6 +70,7 @@ def get_condor_version():
 
     return condor_version
 
+
 def create_directories_hpc(working_dir):
     """
     Function to create a set of directories, given a root directory
@@ -78,7 +83,15 @@ def create_directories_hpc(working_dir):
         print("Error. Working directory {} does not exist! Aborting")
         raise ValueError
 
-    directories_list = ['scripts', 'stdout', 'stderr', 'results', 'logs', 'status', 'joining']
+    directories_list = [
+        "scripts",
+        "stdout",
+        "stderr",
+        "results",
+        "logs",
+        "status",
+        "joining",
+    ]
 
     # Make directories.
     for subdir in directories_list:
@@ -100,6 +113,7 @@ def create_directories_hpc(working_dir):
                 directories_exist = False
     print("..Finished! Directories exist.")
 
+
 def path_of_calling_script():
     """
     Function to get the name of the script the user executes.
@@ -107,6 +121,7 @@ def path_of_calling_script():
 
     return main.__file__
 
+
 def get_python_details():
     """
     Function to get some info about the used python version and virtualenv etc
@@ -115,8 +130,8 @@ def get_python_details():
     python_info_dict = {}
 
     #
-    python_info_dict['virtualenv'] = os.getenv('VIRTUAL_ENV')
-    python_info_dict['executable'] = sys.executable
-    python_info_dict['version'] = sys.version
+    python_info_dict["virtualenv"] = os.getenv("VIRTUAL_ENV")
+    python_info_dict["executable"] = sys.executable
+    python_info_dict["version"] = sys.version
 
     return python_info_dict

coverage.txt

-
-File: "binary_c-python/__init__.py"
- - File is empty
- Needed: 0; Found: 0; Missing: 0; Coverage: 0.0%
-
-File: "binary_c-python/setup.py"
- - No module docstring
- - No docstring for `readme`
- Needed: 2; Found: 0; Missing: 2; Coverage: 0.0%
-
-File: "binary_c-python/examples/example_population.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/examples/examples.py"
- - No module docstring
- Needed: 6; Found: 5; Missing: 1; Coverage: 83.3%
-
-File: "binary_c-python/examples/example_plotting_distributions.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/examples/examples_custom_logging.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/examples/.ipynb_checkpoints/examples-checkpoint.py"
- - No module docstring
- Needed: 5; Found: 4; Missing: 1; Coverage: 80.0%
-
-File: "binary_c-python/snippets/multiprocessing_comparison.py"
- - No module docstring
- - No docstring for `parse_function`
- - No docstring for `evolve_mp`
- - No docstring for `g`
- Needed: 5; Found: 1; Missing: 4; Coverage: 20.0%
-
-File: "binary_c-python/snippets/verbose.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/snippets/test.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/snippets/increment.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/snippets/phasevol.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/snippets/dict_merging.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/snippets/yield_test.py"
- - No module docstring
- - No docstring for `yielder`
- Needed: 2; Found: 0; Missing: 2; Coverage: 0.0%
-
-File: "binary_c-python/snippets/montecarlo_example.py"
- - No module docstring
- - No docstring for `mass_montecarlo`
- - No docstring for `calc_alpha`
- - No docstring for `period_montecarlo`
- - No docstring for `calc_beta`
- - No docstring for `massratio_montecarlo`
- - No docstring for `eccentricity_montecarlo`
- Needed: 7; Found: 0; Missing: 7; Coverage: 0.0%
-
-File: "binary_c-python/snippets/defaultdict.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/snippets/multiprocessing_test.py"
- - No module docstring
- - No docstring for `calculate`
- - No docstring for `calculate.run`
- - No docstring for `run.f`
- Needed: 4; Found: 0; Missing: 4; Coverage: 0.0%
-
-File: "binary_c-python/docs/source/conf.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/lib/__init__.py"
- - File is empty
- Needed: 0; Found: 0; Missing: 0; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/__init__.py"
- - File is empty
- Needed: 0; Found: 0; Missing: 0; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/core/__init__.py"
- - File is empty
- Needed: 0; Found: 0; Missing: 0; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/utils/grid_options_defaults.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/utils/distribution_functions.py"
- - No module docstring
- - No docstring for `calculate_constants_three_part_powerlaw`
- - No docstring for `Arenou2010_binary_fraction`
- Needed: 23; Found: 20; Missing: 3; Coverage: 87.0%
-
-File: "binary_c-python/binarycpython/utils/stellar_types.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/utils/spacing_functions.py"
- - No module docstring
- - No docstring for `const`
- Needed: 2; Found: 0; Missing: 2; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/utils/useful_funcs.py"
- - No module docstring
- Needed: 7; Found: 6; Missing: 1; Coverage: 85.7%
-
-File: "binary_c-python/binarycpython/utils/__init__.py"
- - File is empty
- Needed: 0; Found: 0; Missing: 0; Coverage: 0.0%
-
-File: "binary_c-python/binarycpython/utils/custom_logging_functions.py"
- - No module docstring
- Needed: 9; Found: 8; Missing: 1; Coverage: 88.9%
-
-File: "binary_c-python/binarycpython/utils/functions.py"
- - No module docstring
- - No docstring for `parse_binary_c_version_info`
- Needed: 13; Found: 11; Missing: 2; Coverage: 84.6%
-
-File: "binary_c-python/binarycpython/utils/grid.py"
- - No module docstring
- - No docstring for `Population`
- - No docstring for `Population.set_bse_option`
- - No docstring for `evolve_population_comparison.evolve_mp`
- - No docstring for `evolve_population_comparison.g`
- - No docstring for `evolve_population_mp.evolve_mp`
- - No docstring for `evolve_population_mp.g`
- Needed: 32; Found: 25; Missing: 7; Coverage: 78.1%
-
-File: "binary_c-python/binarycpython/utils/.ipynb_checkpoints/custom_logging_functions-checkpoint.py"
- - No module docstring
- Needed: 9; Found: 8; Missing: 1; Coverage: 88.9%
-
-File: "binary_c-python/binarycpython/utils/.ipynb_checkpoints/functions-checkpoint.py"
- - No module docstring
- - No docstring for `load_logfile`
- Needed: 8; Found: 6; Missing: 2; Coverage: 75.0%
-
-File: "binary_c-python/tests/python_API_test.py"
- - No module docstring
- - No docstring for `test_run_binary`
- - No docstring for `test_return_help`
- - No docstring for `test_return_arglines`
- - No docstring for `test_run_binary_with_log`
- - No docstring for `test_run_binary_with_custom_logging`
- - No docstring for `test_return_help_all`
- - No docstring for `test_return_version_info`
- - No docstring for `test_return_store`
- - No docstring for `test_run_system`
- Needed: 10; Found: 0; Missing: 10; Coverage: 0.0%
-
-File: "binary_c-python/tests/random_tests.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/tests/function_tests.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/tests/population/plot_scaling.py"
- - No module docstring
- - No docstring for `calc_mean_and_std`
- Needed: 2; Found: 0; Missing: 2; Coverage: 0.0%
-
-File: "binary_c-python/tests/population/grid_tests_cmdline.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/tests/population/multiprocessing_via_population_comparison.py"
- - No module docstring
- - No docstring for `parse_function`
- Needed: 3; Found: 1; Missing: 2; Coverage: 33.3%
-
-File: "binary_c-python/tests/population/grid_tests.py"
- - No module docstring
- Needed: 1; Found: 0; Missing: 1; Coverage: 0.0%
-
-File: "binary_c-python/tests/population/global_variable_for_distributions.py"
- - No module docstring
- - No docstring for `with_glob`
- - No docstring for `without_glob`
- Needed: 6; Found: 3; Missing: 3; Coverage: 50.0%
-
-File: "binary_c-python/.ipynb_checkpoints/python_API_test-checkpoint.py"
- - No module docstring
- - No docstring for `run_test_binary`
- Needed: 2; Found: 0; Missing: 2; Coverage: 0.0%
-
-
-Overall statistics for 41 files (5 files are empty):
-Docstrings needed: 173; Docstrings found: 98; Docstrings missing: 75
-Total docstring coverage: 56.6%;  Grade: Not bad

tests/core/test_persistent_data.py

@@ -68,6 +68,7 @@ def test_return_persistent_data_memaddr():
     assert isinstance(output, int), "memory adress has to be an integer"
     assert output != 0, "memory adress seems not to have a correct value"
 
+
 def test_passing_persistent_data_to_run_system():
     # Function to test the passing of the persistent data memoery adress, and having ensemble_defer = True
     # We should see that the results of multiple systems have been added to the one output json
@@ -292,8 +293,6 @@ def test_adding_ensemble_output():
     # print(json.dumps(test_1_merged_dict, indent=4))
     # print(json.dumps(test_2_json, indent=4))
 
-
-
     #
     assert inspect_dict(test_1_merged_dict, print_structure=False) == inspect_dict(
         test_2_json, print_structure=False
@@ -359,6 +358,7 @@ def test_free_and_json_output():
     # ensemble_jsons_1 = [line for line in output_1.splitlines() if line.startswith("ENSEMBLE_JSON")]
     # json_1 = json.loads(ensemble_jsons_1[0][len("ENSEMBLE_JSON "):], cls=binarycDecoder)
 
+
 def test_all():
     test_return_persistent_data_memaddr()
     test_passing_persistent_data_to_run_system()
@@ -367,6 +367,7 @@ def test_all():
     test_free_and_json_output()
     test_combine_with_empty_json()
 
+
 ####
 if __name__ == "__main__":
     # test_return_persistent_data_memaddr()

tests/core/test_return_store_memaddr.py

@@ -9,6 +9,7 @@ def test_return_store_memaddr():
     print("store memory adress:")
     print(textwrap.indent(str(output), "\t"))
 
+
 def test_unload_store_memaddr():
     output = binary_c_python_api.return_store_memaddr()
 
@@ -19,6 +20,7 @@ def test_unload_store_memaddr():
     _ = binary_c_python_api.free_store_memaddr(output)
     print("freed store memaddr")
 
+
 ####
 if __name__ == "__main__":
     test_return_store_memaddr()