render docs

_reference/cmd.qmd

@@ -34,7 +34,8 @@ Run KIMMDY from the command line.
 
 The configuration is gathered from the input file,
 which is `kimmdy.yml` by default.
-See [](`~kimmdy.cmd.get_cmdline_args`) or `kimmdy --help` for the descriptions of the arguments.
+See [](`~kimmdy.cmd.get_cmdline_args`) or `kimmdy --help`
+for the descriptions of the arguments.
 
 ### get_cmdline_args { #kimmdy.cmd.get_cmdline_args }
 
@@ -50,7 +51,7 @@ Parse command line arguments.
 
 ### kimmdy_run { #kimmdy.cmd.kimmdy_run }
 
-`cmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, checkpoint='', show_plugins=False, show_schema_path=False, generate_jobscript=False, debug=False)`
+`cmd.kimmdy_run(input=Path('kimmdy.yml'), loglevel=None, logfile=None, checkpoint='', show_plugins=False, show_schema_path=False, generate_jobscript=False, debug=False, callgraph=False)`
 
 Run KIMMDY from python.
 

_reference/config.qmd

@@ -37,13 +37,13 @@ and computationally expensive operations.
 
 ##### attr { #kimmdy.config.Config.attr }
 
-`config.Config.attr(attribute)`
+`config.Config.attr(self, attribute)`
 
 Get the value of a specific attribute.
 Alias for self.__getattribute__
 
 ##### get_attributes { #kimmdy.config.Config.get_attributes }
 
-`config.Config.get_attributes()`
+`config.Config.get_attributes(self)`
 
 Get a list of all attributes without hidden ones (_<...>).

_reference/parsing.qmd

@@ -224,10 +224,6 @@ raw_top =
 
 `parsing.resolve_includes(path, gmx_builtin_ffs=None)`
 
-Resolve #include statements in a (top/itp) file.
-
-
-
 #### Arguments
 
 path :

_reference/plugins.qmd

@@ -27,7 +27,7 @@ reconstruct base force field state
 
 ##### parameterize_topology { #kimmdy.plugins.BasicParameterizer.parameterize_topology }
 
-`plugins.BasicParameterizer.parameterize_topology(current_topology)`
+`plugins.BasicParameterizer.parameterize_topology(self, current_topology)`
 
 Do nothing,
 all necessary actions should already have happened in bind_bond and break_bond of Topology
@@ -53,7 +53,7 @@ Reaction base class
 
 ##### get_recipe_collection { #kimmdy.plugins.ReactionPlugin.get_recipe_collection }
 
-`plugins.ReactionPlugin.get_recipe_collection(files)`
+`plugins.ReactionPlugin.get_recipe_collection(self, files)`
 
 Get a RecipeCollection as a result of the reaction.
 

_reference/recipe.qmd

@@ -114,7 +114,7 @@ product state from the educt state.
 
 ##### calc_averages { #kimmdy.recipe.Recipe.calc_averages }
 
-`recipe.Recipe.calc_averages(window_size)`
+`recipe.Recipe.calc_averages(self, window_size)`
 
 Calulate average rates over some window size
 
@@ -126,13 +126,13 @@ Calulate average rates over some window size
 
 ##### check_consistency { #kimmdy.recipe.Recipe.check_consistency }
 
-`recipe.Recipe.check_consistency()`
+`recipe.Recipe.check_consistency(self)`
 
 Run consistency checks for correct size of variables
 
 ##### combine_with { #kimmdy.recipe.Recipe.combine_with }
 
-`recipe.Recipe.combine_with(other)`
+`recipe.Recipe.combine_with(self, other)`
 
 Combines this Recipe with another with the same RecipeSteps.
 
@@ -168,21 +168,21 @@ They can originate from multiple reaction plugins, but do not need to.
 
 ##### aggregate_reactions { #kimmdy.recipe.RecipeCollection.aggregate_reactions }
 
-`recipe.RecipeCollection.aggregate_reactions()`
+`recipe.RecipeCollection.aggregate_reactions(self)`
 
 Combines reactions having the same sequence of RecipeSteps.
 
 ##### calc_cumprob { #kimmdy.recipe.RecipeCollection.calc_cumprob }
 
-`recipe.RecipeCollection.calc_cumprob()`
+`recipe.RecipeCollection.calc_cumprob(self)`
 
 Calculate cumulative probability of all contained recipe steps.
 Sums up to 1 over all recipes. Assumes constant rate for given timespan
 and rate zero otherwise.
 
 ##### calc_ratesum { #kimmdy.recipe.RecipeCollection.calc_ratesum }
 
-`recipe.RecipeCollection.calc_ratesum()`
+`recipe.RecipeCollection.calc_ratesum(self)`
 
 Calculate the sum of rates over all timesteps
 
@@ -196,14 +196,14 @@ Calculate the sum of rates over all timesteps
 
 ##### from_csv { #kimmdy.recipe.RecipeCollection.from_csv }
 
-`recipe.RecipeCollection.from_csv(path)`
+`recipe.RecipeCollection.from_csv(cls, path)`
 
 Create a RecipeCollection object from a CSV file
 Returns the recipe collection and a single recipe that was picked, otherwise None
 
 ##### plot { #kimmdy.recipe.RecipeCollection.plot }
 
-`recipe.RecipeCollection.plot(outfile, highlight_r=None, highlight_t=None)`
+`recipe.RecipeCollection.plot(self, outfile, highlight_r=None, highlight_t=None)`
 
 Plot reaction rates over time
 
@@ -217,7 +217,7 @@ Plot reaction rates over time
 
 ##### to_csv { #kimmdy.recipe.RecipeCollection.to_csv }
 
-`recipe.RecipeCollection.to_csv(path, picked_recipe=None)`
+`recipe.RecipeCollection.to_csv(self, path, picked_recipe=None)`
 
 Write a ReactionResult as defined in the reaction module to a csv file
 

_reference/runmanager.qmd

@@ -51,7 +51,7 @@ rest of the program and keeps track of global state.
 
 ##### get_latest { #kimmdy.runmanager.RunManager.get_latest }
 
-`runmanager.RunManager.get_latest(suffix)`
+`runmanager.RunManager.get_latest(self, suffix)`
 
 Returns path to latest file of given type.
 
@@ -60,7 +60,7 @@ Errors if file is not found.
 
 ##### write_one_checkpoint { #kimmdy.runmanager.RunManager.write_one_checkpoint }
 
-`runmanager.RunManager.write_one_checkpoint()`
+`runmanager.RunManager.write_one_checkpoint(self)`
 
 Just write the first checkpoint and then exit
 

_reference/tasks.qmd

@@ -23,14 +23,6 @@ Dictionary that gets populated by calling get_missing.
 
 `tasks.Task(self, runmng, f, kwargs=None, out=None)`
 
-A task to be performed as as a step in the RunManager.
-
-A task consists of a function and its keyword arguments.
-Calling a taks calls the stored function.
-The function must return a TaskFiles object.
-
-
-
 #### Parameters:
 
 runmng
@@ -46,17 +38,6 @@ out
 
 `tasks.TaskFiles(get_latest, input=field(default_factory=dict), output=field(default_factory=dict), outputdir=Path(), logger=logging.getLogger('kimmdy.basetask'))`
 
-Class for Task input and output files and directories.
-
-Hosts the input and output file paths belonging to a task.
-A function or method that wants to be callable as a Task
-has to return a TaskFiles object.
-The input defaultdict is populated on the fly using
-get_latest of the runmanager to find newest files.
-Files which can not be found by get_latest must be added manually.
-
-
-
 #### Atributes
 
 get_latest:

_reference/topology.topology.qmd

@@ -40,7 +40,7 @@ One moleculetype in the topology
 
 ##### reindex_atomnrs { #kimmdy.topology.topology.MoleculeType.reindex_atomnrs }
 
-`topology.topology.MoleculeType.reindex_atomnrs()`
+`topology.topology.MoleculeType.reindex_atomnrs(self)`
 
 Reindex atom numbers in topology.
 
@@ -50,7 +50,7 @@ Returns a dict, mapping of old atom number strings to new ones
 
 ##### test_for_radicals { #kimmdy.topology.topology.MoleculeType.test_for_radicals }
 
-`topology.topology.MoleculeType.test_for_radicals()`
+`topology.topology.MoleculeType.test_for_radicals(self)`
 
 Updates radical status per atom and in topology.
 
@@ -89,7 +89,7 @@ Assumptions:
 
 ##### bind_bond { #kimmdy.topology.topology.Topology.bind_bond }
 
-`topology.topology.Topology.bind_bond(atompair_addresses)`
+`topology.topology.Topology.bind_bond(self, atompair_addresses)`
 
 Add a bond in topology.
 
@@ -106,7 +106,7 @@ Furthermore, it modifies to function types in the topology to account for radica
 
 ##### break_bond { #kimmdy.topology.topology.Topology.break_bond }
 
-`topology.topology.Topology.break_bond(atompair_addresses)`
+`topology.topology.Topology.break_bond(self, atompair_addresses)`
 
 Break bonds in topology homolytically.
 
@@ -122,7 +122,7 @@ Atom pairs become radicals.
 
 ##### del_atom { #kimmdy.topology.topology.Topology.del_atom }
 
-`topology.topology.Topology.del_atom(atom_nr, parameterize=True)`
+`topology.topology.Topology.del_atom(self, atom_nr, parameterize=True)`
 
 Deletes atom
 
@@ -144,7 +144,7 @@ parameters if requested.
 
 ##### reindex_atomnrs { #kimmdy.topology.topology.Topology.reindex_atomnrs }
 
-`topology.topology.Topology.reindex_atomnrs()`
+`topology.topology.Topology.reindex_atomnrs(self)`
 
 Reindex atom numbers in topology.
 
@@ -154,7 +154,7 @@ Returns a dict of all moleculetypes to their update maps (old -> new).
 
 ##### validate_bond { #kimmdy.topology.topology.Topology.validate_bond }
 
-`topology.topology.Topology.validate_bond(atm1, atm2)`
+`topology.topology.Topology.validate_bond(self, atm1, atm2)`
 
 Validates bond consistency between both atoms and top
 Returns True if bond exists, False if not.