{"action":"created","comment":{"url":"https://api.github.com/repos/sg-s/xolotl/pulls/comments/192929297","pull_request_review_id":125799999,"id":192929297,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDE5MjkyOTI5Nw==","diff_hunk":"@@ -0,0 +1,444 @@\n+.. set up matlab code highlighting\n+.. highlight:: matlab\n+\n+.. set up referencing\n+.. _methods:\n+\n+Methods\n+=======\n+\n+This documentation will focus on using ``xolotl`` in ``MATLAB``, though it is\n+possible to compile and run the ``C++`` code on its own.\n+\n+A ``xolotl`` object can be instantiated ::\n+\n+  x = xolotl;\n+\n+For consistency, this documentation will assume a ``xolotl`` object named ``x``.\n+\n+.. hint::\n+\n+  You can list all the methods of ``xolotl`` object ``x`` by ::\n+\n+    x.methods\n+\n+.. _children:\n+\n+Children\n+^^^^^^^^\n+\n+Returns the children of any ``cpplab`` object as a cell of character vectors.\n+Children are also ``cpplab`` objects. For example, if ``HH`` is the only compartment in ``x`` then ::\n+\n+  x.Children\n+\n+returns ::\n+\n+  {'HH'}\n+\n+This method is inherited from the superclass ``cpplab``.\n+\n+.. _add:\n+\n+add\n+^^^\n+\n+Adds a compartment, conductance, or synapse to the ``xolotl`` object. To add\n+a compartment::\n+\n+  x.add('compartmentName','compartment','PropertyName','PropertyValue', ...)\n+\n+Valid compartment properties are\n+\n+======================= ================\n+Name                    ``PropertyName``\n+Volume                  ``vol``\n+Surface area            ``A``\n+Extra. calcium steady.  ``Ca_out``\n+Buffer shell thickness  ``shell_thickness``\n+Intra. calcium steady.  ``Ca_in``\n+Ca++ curr. to conc.     ``phi``\n+Average Ca++ conc.      ``Ca_average``\n+Radius of compartment   ``radius``\n+Target Ca++ conc.       ``Ca_target``\n+Index in `xolotl` tree  ``tree_idx``\n+Index of neuron         ``neuron_idx``\n+Length of compartment   ``len``\n+Ca++ buff. time const.  ``tau_Ca``\n+Membrane capacitance    ``Cm``\n+Intra. calcium conc.    ``Ca``\n+Membrane potential      ``V``\n+======================= ================\n+\n+To add a compartment named ``HH`` with a membrane capacitance ``Cm = 10`` ::\n+\n+  x.add('HH', 'compartment', 'Cm', 10);\n+\n+To access properties of that compartment, use the syntax ``x.HH``. To add a conductance to that compartment ::\n+\n+  x.HH.add('ConductancePath', 'PropertyName', 'PropertyValue', ...);\n+\n+``ConductancePath`` is the path to the ``.hpp`` file inside ``xolotl/c++/conductances/``. For example, the conductance path to add the slow calcium conductance from Prinz *et al.* 2003 is ``prinz/CaS`` since the conductance is specified in ``xolotl/c++/conductances/prinz/CaS.hpp``.\n+\n+The following properties can be specified\n+\n+======================= ================\n+Name                    ``PropertyName``\n+Maximal conductance     ``gbar``\n+Reversal potential      ``E``\n+Inactivation variable   ``h``\n+Activation variable     ``m``\n+======================= ================\n+\n+For example ::\n+\n+  x.HH.add('prinz/CaS', 'gbar', 500, 'E', -80);\n+\n+The maximal conductance defaults to 0, the reversal potential defaults based on\n+the conductance. Activation variables (if any) default to zero. Inactivation variables\n+default to one. Synapses can be added this way, but it is better to use the ``connect`` method.\n+\n+.. _cleanup:\n+\n+cleanup\n+^^^^^^^\n+\n+When the ``C++`` code compiles, it produces a binary ``.mexa64`` file and a ``.cpp`` file in your ``xolotl`` directory. These files are hashed so that repeated simulation does not require recompilation. If these files are too numerous or broken, you can erase them all by calling either ::\n+\n+  xolotl.cleanup\n+  x.cleanup\n+\n+\n+.. _compile:\n+\n+compile\n+^^^^^^^\n+\n+Hashes and compiles the files needed to run a simulation. These are stored in\n+your ``xolotl`` directory. ``xolotl`` automatically compiles when it needs to.\n+You can turn this functionally off by setting ::\n+\n+  x.skip_hash = true;\n+\n+In addition, creating a ``xolotl`` object through a function call does not\n+automatically hash and compile. In this case, you should use ``x.md5hash``.\n+=======\n+In addition, creating a ``xolotl`` object through a function call does not automatically hash and compile. In this case, you should use ``x.md5hash``.\n+>>>>>>> 2c44bd81aed5d11aac7fb1677a4b462d47822744\n+\n+.. hint::\n+\n+  Always transpile before you compile! ::\n+\n+    x.transpile;\n+    x.compile;\n+\n+.. _connect:\n+\n+connect\n+^^^^^^^\n+\n+Connects two compartments with a synapse. The basic syntax is ::\n+\n+  x.connect('PreSynaptic', 'PostSynaptic', 'Type', PropertyName', PropertyValue, ...)\n+\n+The first two arguments are the presynaptic and postsynaptic compartment names.\n+\n+In the case of two arguments, or three arguments where the third is a ``double``,\n+an axial or electrical synapse is created between the two compartments. An axial\n+synapse is created if either of the compartments is part of a spacially-discretized\n+multi-compartment structure (e.g. has a defined ``tree_idx``). Otherwise, the created\n+synapse is electrical. Axial and electrical synapses differ in how they are integrated\n+(see Dayan & Abbott 2001, Ch. 5-6). ::\n+\n+  % create a synapse between AB and LP with gbar of NaN\n+  x.connect('AB', 'LP')\n+  % create a synapse between AB and LP with gbar of 10\n+  x.connect('AB', 'LP', 10)\n+\n+The most common way to produce a synapse is to pass the synapse type and then any\n+properties. For example, to add a glutamatergic synapse between ``AB`` and ``LP``\n+with a maximal conductance of 100: ::\n+\n+  x.connect('AB', 'LP', 'Glut', 'gbar', 100)\n+\n+\n+Synapses can also be connected by passing a ``cpplab`` object to the ``connect``\n+function ::\n+\n+  % create a synapse using the cpplab object 'syn_cpplab'\n+  x.connect('AB', 'LP', syn_cpplab)\n+\n+The following properties can be specified\n+\n+======================= ================\n+Name                    ``PropertyName``\n+Maximal conductance     ``gbar``\n+Reversal potential      ``E``\n+Activation variable     ``s``\n+======================= ================\n+=======\n+Connects two compartments with a synapse. This defaults to an electrical synapse with axial conductance of ``NaN``.\n+\n+Connect two compartments ``AB`` and ``PD`` with an axial conductance of ``NaN`` ::\n+\n+  x.connect('AB', 'PD')\n+\n+Connect two compartments with an axial conductance of ``gAxial`` ::\n+\n+  x.connect('AB', 'PD', gAxial)\n+\n+Connect two compartments with a glutamatergic synapse with maximal conductance ``gGlut`` ::\n+\n+  x.connect('AB', 'PD', 'Glut', gGlut)\n+>>>>>>> 2c44bd81aed5d11aac7fb1677a4b462d47822744\n+\n+.. _copy:\n+\n+copy\n+^^^^\n+\n+Copies the entirety of a ``cpplab`` object into a new variable. ::\n+\n+  % create a new xolotl object\n+  N = x.copy\n+  % create a new HH object\n+  N = x.HH.copy\n+\n+.. _get:\n+\n+get\n+^^^\n+::\n+\n+  values = x.get('findString')\n+\n+Returns a vector of doubles of the values stored in the specified fields. Automatically calls the ``find`` function; the argument is a search query for the ``find`` function. ::\n+\n+  % find all maximal conductances\n+  gbars = x.get('*gbar')\n+  % find all maximal conductances in HH compartment\n+\n+Produces a vector which contains the values of specified properties. ``get`` implicitly calls ``find`` and uses it to identify and order the elements of the vector. For this reason, ``get`` uses wildcard string comprehension. For example, ``'HH*gbar'`` means anything that begins with ``'HH'`` and ends with ``'gbar'``.\n+Find all the maximal conductances of the ``HH`` compartment ::\n+\n+  gbars = x.get('HH*gbar')\n+\n+.. _find:\n+\n+find\n+^^^^\n+\n+::\n+\n+  x.find('findString')\n+\n+Returns a cell array of character vectors for a search query. This function is a ``cpplab`` method, so what it does is specific to in which scope it is called.\n+For example, for a xolotl object ``x`` with a compartment ``HH`` with three conductances ``NaV, Kd, Leak`` ::\n+\n+  x.find('*gbar')\n+\n+returns ::\n+\n+  {'HH.Kd.gbar'  }\n+  {'HH.Leak.gbar'}\n+  {'HH.NaV.gbar' }\n+\n+whereas, a call within the ``HH`` scope ::\n+\n+  x.HH.find('*gbar')\n+\n+yields ::\n+\n+  {'Kd.gbar'  }\n+  {'Leak.gbar'}\n+  {'NaV.gbar' }\n+\n+The ``*`` symbol is the wildcard operator. It finds any string that matches that pattern (e.g. ``*gbar`` finds any string in the ``xolotl`` tree that ends with ``'gbar'``).\n+For example, ``x.find('HH*gbar')`` would only fetch paths to maximal conductances in the ``HH`` compartment.\n+\n+.. hint::\n+\n+  The ``set`` and ``get`` functions use the same syntax as the ``find`` function. They call it implicitly.\n+\n+.. _getGatingFunctions:\n+\n+getGatingFunctions\n+^^^^^^^^^^^^^^^^^^\n+\n+::\n+\n+  [act ict tau_act tau_ict] = xolotl.getGatingFunctions('conductancePath')\n+\n+Returns the gating functions of a conductance as function handles. The function has four outputs.\n+The activation steady state equation comes first, followed by the inactivation steady state (if any), then the activation time constant, and finally the inactivation time constant (if any).\n+The argument is a string that specifies where in the file directory the conductance is specified.\n+For example to find the ``NaV`` conductance from Liu *et al.* 1998, which is detailed in\n+``.../xolotl/c++/conductances/liu/NaV.hpp`` ::\n+\n+  [m_inf, h_inf, tau_m, tau_h] = x.getGatingFunctions('liu/NaV')\n+\n+.. hint::\n+\n+  This is a static method of ``xolotl`` (i.e. ``xolotl.getGatingFunctions(...)`` is valid).\n+\n+.. _integrate:\n+\n+integrate\n+^^^^^^^^^\n+\n+::\n+\n+  [V, Ca, cont_states, currents, syn_currents] = x.integrate\n+\n+Integrates the ``xolotl`` object. Returns the membrane potential, intracellular calcium, controller states, intrinsic currents, and synaptic currents as time series.\n+\n+The membrane potential is returned as matrix of ``time steps x compartments`` in the same order as the ``xolotl`` object's scalar representation (i.e. in the command window).\n+The intracellular calcium is returned as a matrix of ``time steps x 2*compartments``. The first *n* time series are the intracellular calcium concentrations for each compartment, and the second *n* time series are the instantaneous calcium reversal potentials.\n+Controller states are returned as a matrix of ``time steps x 2*controllers`` where the first column in each two-column pair is the controller state and the second is the state of the thing upon which the controller is operating.\n+For a controller onto a maximal conductance, for instance, the first column is the controller state and the second is the maximal conductance.\n+All other outputs are ``time series x XYZ`` where XYZ is the serialized list of those properties. For example, in a ``xolotl`` object with 2 compartments ``AB`` and ``BC``\n+with two conductances each: ``NaV`` and ``Kd``, the intrinsic currents would return in the form of a ``time steps x 4`` matrix where the columns would be ordered:\n+Kd current from AB, NaV current from AB, Kd current from BC, NaV current from BC.\n+\n+If ``integrate`` is passed one argument, it interprets this as a matrix of injected currents (in nA). For example ::\n+\n+  % applies 0.2 nA to each compartment\n+  x.integrate(0.2)\n+  % applies 0.2 nA to first compartment of three\n+  x.integrate([0.2 0 0])\n+  % applies a time-varying current to first compartment\n+  % where time is a vector of length x.t_end / x.dt\n+  x.integrate([0.2*sin(time); zeros(time); zeros(time)])","path":"docs/_build/html/_sources/methods.rst.txt","position":312,"original_position":312,"commit_id":"c3cdf9391c83f2e7bc477437d6149722d5b1e25d","original_commit_id":"37f2907df40d60db190d68394f1ae268549ea7db","user":{"login":"alec-hoyland","id":30243182,"node_id":"MDQ6VXNlcjMwMjQzMTgy","avatar_url":"https://avatars3.githubusercontent.com/u/30243182?v=4","gravatar_id":"","url":"https://api.github.com/users/alec-hoyland","html_url":"https://github.com/alec-hoyland","followers_url":"https://api.github.com/users/alec-hoyland/followers","following_url":"https://api.github.com/users/alec-hoyland/following{/other_user}","gists_url":"https://api.github.com/users/alec-hoyland/gists{/gist_id}","starred_url":"https://api.github.com/users/alec-hoyland/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alec-hoyland/subscriptions","organizations_url":"https://api.github.com/users/alec-hoyland/orgs","repos_url":"https://api.github.com/users/alec-hoyland/repos","events_url":"https://api.github.com/users/alec-hoyland/events{/privacy}","received_events_url":"https://api.github.com/users/alec-hoyland/received_events","type":"User","site_admin":false},"body":"done","created_at":"2018-06-05T02:17:05Z","updated_at":"2018-06-05T02:17:05Z","html_url":"https://github.com/sg-s/xolotl/pull/130#discussion_r192929297","pull_request_url":"https://api.github.com/repos/sg-s/xolotl/pulls/130","author_association":"COLLABORATOR","_links":{"self":{"href":"https://api.github.com/repos/sg-s/xolotl/pulls/comments/192929297"},"html":{"href":"https://github.com/sg-s/xolotl/pull/130#discussion_r192929297"},"pull_request":{"href":"https://api.github.com/repos/sg-s/xolotl/pulls/130"}},"in_reply_to_id":192816981},"pull_request":{"url":"https://api.github.com/repos/sg-s/xolotl/pulls/130","id":192260843,"node_id":"MDExOlB1bGxSZXF1ZXN0MTkyMjYwODQz","html_url":"https://github.com/sg-s/xolotl/pull/130","diff_url":"https://github.com/sg-s/xolotl/pull/130.diff","patch_url":"https://github.com/sg-s/xolotl/pull/130.patch","issue_url":"https://api.github.com/repos/sg-s/xolotl/issues/130","number":130,"state":"open","locked":false,"title":"Add general info to documentation","user":{"login":"alec-hoyland","id":30243182,"node_id":"MDQ6VXNlcjMwMjQzMTgy","avatar_url":"https://avatars3.githubusercontent.com/u/30243182?v=4","gravatar_id":"","url":"https://api.github.com/users/alec-hoyland","html_url":"https://github.com/alec-hoyland","followers_url":"https://api.github.com/users/alec-hoyland/followers","following_url":"https://api.github.com/users/alec-hoyland/following{/other_user}","gists_url":"https://api.github.com/users/alec-hoyland/gists{/gist_id}","starred_url":"https://api.github.com/users/alec-hoyland/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/alec-hoyland/subscriptions","organizations_url":"https://api.github.com/users/alec-hoyland/orgs","repos_url":"https://api.github.com/users/alec-hoyland/repos","events_url":"https://api.github.com/users/alec-hoyland/events{/privacy}","received_events_url":"https://api.github.com/users/alec-hoyland/received_events","type":"User","site_admin":false},"body":"Some of the method syntax is wishful thinking (see `integrate` and `manipulate` in particular), but otherwise this is ready to go live. Consider this beta documentation.","created_at":"2018-06-03T18:32:00Z","updated_at":"2018-06-05T02:17:05Z","closed_at":null,"merged_at":null,"merge_commit_sha":"871e22a6709479a7708f829d57a948cfd041616a","assignee":{"login":"sg-s","id":6005346,"node_id":"MDQ6VXNlcjYwMDUzNDY=","avatar_url":"https://avatars3.githubusercontent.com/u/6005346?v=4","gravatar_id":"","url":"https://api.github.com/users/sg-s","html_url":"https://github.com/sg-s","followers_url":"https://api.github.com/users/sg-s/followers","following_url":"https://api.github.com/users/sg-s/following{/other_user}","gists_url":"https://api.github.com/users/sg-s/gists{/gist_id}","starred_url":"https://api.github.com/users/sg-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sg-s/subscriptions","organizations_url":"https://api.github.com/users/sg-s/orgs","repos_url":"https://api.github.com/users/sg-s/repos","events_url":"https://api.github.com/users/sg-s/events{/privacy}","received_events_url":"https://api.github.com/users/sg-s/received_events","type":"User","site_admin":false},"assignees":[{"login":"sg-s","id":6005346,"node_id":"MDQ6VXNlcjYwMDUzNDY=","avatar_url":"https://avatars3.githubusercontent.com/u/6005346?v=4","gravatar_id":"","url":"https://api.github.com/users/sg-s","html_url":"https://github.com/sg-s","followers_url":"https://api.github.com/users/sg-s/followers","following_url":"https://api.github.com/users/sg-s/following{/other_user}","gists_url":"https://api.github.com/users/sg-s/gists{/gist_id}","starred_url":"https://api.github.com/users/sg-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sg-s/subscriptions","organizations_url":"https://api.github.com/users/sg-s/orgs","repos_url":"https://api.github.com/users/sg-s/repos","events_url":"https://api.github.com/users/sg-s/events{/privacy}","received_events_url":"https://api.github.com/users/sg-s/received_events","type":"User","site_admin":false}],"requested_reviewers":[],"requested_teams":[],"labels":[{"id":927128342,"node_id":"MDU6TGFiZWw5MjcxMjgzNDI=","url":"https://api.github.com/repos/sg-s/xolotl/labels/essential-for-paper","name":"essential-for-paper","color":"006b75","default":false},{"id":699318098,"node_id":"MDU6TGFiZWw2OTkzMTgwOTg=","url":"https://api.github.com/repos/sg-s/xolotl/labels/must-have","name":"must-have","color":"fbca04","default":false}],"milestone":null,"commits_url":"https://api.github.com/repos/sg-s/xolotl/pulls/130/commits","review_comments_url":"https://api.github.com/repos/sg-s/xolotl/pulls/130/comments","review_comment_url":"https://api.github.com/repos/sg-s/xolotl/pulls/comments{/number}","comments_url":"https://api.github.com/repos/sg-s/xolotl/issues/130/comments","statuses_url":"https://api.github.com/repos/sg-s/xolotl/statuses/c3cdf9391c83f2e7bc477437d6149722d5b1e25d","head":{"label":"sg-s:add-general-info-to-documentation","ref":"add-general-info-to-documentation","sha":"c3cdf9391c83f2e7bc477437d6149722d5b1e25d","user":{"login":"sg-s","id":6005346,"node_id":"MDQ6VXNlcjYwMDUzNDY=","avatar_url":"https://avatars3.githubusercontent.com/u/6005346?v=4","gravatar_id":"","url":"https://api.github.com/users/sg-s","html_url":"https://github.com/sg-s","followers_url":"https://api.github.com/users/sg-s/followers","following_url":"https://api.github.com/users/sg-s/following{/other_user}","gists_url":"https://api.github.com/users/sg-s/gists{/gist_id}","starred_url":"https://api.github.com/users/sg-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sg-s/subscriptions","organizations_url":"https://api.github.com/users/sg-s/orgs","repos_url":"https://api.github.com/users/sg-s/repos","events_url":"https://api.github.com/users/sg-s/events{/privacy}","received_events_url":"https://api.github.com/users/sg-s/received_events","type":"User","site_admin":false},"repo":{"id":104088673,"node_id":"MDEwOlJlcG9zaXRvcnkxMDQwODg2NzM=","name":"xolotl","full_name":"sg-s/xolotl","owner":{"login":"sg-s","id":6005346,"node_id":"MDQ6VXNlcjYwMDUzNDY=","avatar_url":"https://avatars3.githubusercontent.com/u/6005346?v=4","gravatar_id":"","url":"https://api.github.com/users/sg-s","html_url":"https://github.com/sg-s","followers_url":"https://api.github.com/users/sg-s/followers","following_url":"https://api.github.com/users/sg-s/following{/other_user}","gists_url":"https://api.github.com/users/sg-s/gists{/gist_id}","starred_url":"https://api.github.com/users/sg-s/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sg-s/subscriptions","organizations_url":"https://api.github.com/users/sg-s/orgs","repos_url":"https://api.github.com/users/sg-s/repos","events_url":"https://api.github.com/users/sg-s/events{/privacy}","received_events_url":"https://api.github.com/users/sg-s/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/sg-s/xolotl","description":"xolotl: the standard neuron simulator. 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