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Merge pull request #502 in ENG/mies-igor from ~THOMASB/mies-igor:feat…
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…ure/switch_to_sphinx_breathe_for_documentation_generation to master

* commit '68943b8cc7cc614e3e0bbe50c783d592d6f65f8f':
  Doc: Switch to doxygen, breathe and sphinx for documentation generation
  GetDA_EphysGuiStateNum: Fix list in comment
  Doc: Add misc.rst
  NWB.md: Convert to rst
  Doxygen: Fix code/verbatim blocks
  README/ReleaseNotes.md: Fix some markup issues
  mainpage.md: Convert to index.rst
  Doxygen: Enable XML output
  doxygen-filter-ipf: Make output sphinx compatible

Original-CommitID: ecdcaaed1b73a28a7958f7dc260b90ef8163ad14
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t-b committed Oct 17, 2016
2 parents 044ac1c + 68943b8 commit 07064cb
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Showing 18 changed files with 502 additions and 342 deletions.
50 changes: 25 additions & 25 deletions Packages/IPNWB/IPNWB_Debugging.ipf
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Expand Up @@ -14,11 +14,11 @@
/// @param errorMsg error message to output in failure case
///
/// Example usage:
///@code
///ControlInfo/W = $panelTitle popup_MoreSettings_DeviceType
///ASSERT(V_flag > 0, "Non-existing control or window")
///do something with S_value
///@endcode
/// @code
/// ControlInfo/W = $panelTitle popup_MoreSettings_DeviceType
/// ASSERT(V_flag > 0, "Non-existing control or window")
/// do something with S_value
/// @endcode
///
/// @hidecallgraph
/// @hidecallergraph
Expand Down Expand Up @@ -63,14 +63,14 @@ static StrConstant functionReturnMessage = "return value"
/// Debug function especially designed for usage in return statements.
///
/// For example calling the following function
///@code
///Function doStuff()
/// variable var = 1 + 2
/// return DEBUGPRINTv(var)
///End
///@endcode
/// @code
/// Function doStuff()
/// variable var = 1 + 2
/// return DEBUGPRINTv(var)
/// End
/// @endcode
/// will output
///@verbatim DEBUG doStuff(...)#L5: return value 3 @endverbatim
/// @verbatim DEBUG doStuff(...)#L5: return value 3 @endverbatim
/// to the history.
///
/// @hidecallgraph
Expand All @@ -96,14 +96,14 @@ End
/// Debug function especially designed for usage in return statements.
///
/// For example calling the following function
///@code
///Function/s doStuff()
/// variable str= "a" + "b"
/// return DEBUGPRINTs(str)
///End
///@endcode
/// @code
/// Function/s doStuff()
/// variable str= "a" + "b"
/// return DEBUGPRINTs(str)
/// End
/// @endcode
/// will output
///@verbatim DEBUG doStuff(...)#L5: return value ab @endverbatim
/// @verbatim DEBUG doStuff(...)#L5: return value ab @endverbatim
/// to the history.
///
/// @hidecallgraph
Expand All @@ -128,12 +128,12 @@ End
/// Outputs variables and strings with optional format argument.
///
///Examples:
///@code
///DEBUGPRINT("before a possible crash")
///DEBUGPRINT("some variable", var=myVariable)
///DEBUGPRINT("my string", str=myString)
///DEBUGPRINT("Current state", var=state, format="%.5f")
///@endcode
/// @code
/// DEBUGPRINT("before a possible crash")
/// DEBUGPRINT("some variable", var=myVariable)
/// DEBUGPRINT("my string", str=myString)
/// DEBUGPRINT("Current state", var=state, format="%.5f")
/// @endcode
///
/// @hidecallgraph
/// @hidecallergraph
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50 changes: 27 additions & 23 deletions Packages/IPNWB/IPNWB_Utils.ipf
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Expand Up @@ -74,30 +74,34 @@ End
/// @param[out] numPrefix numerical value of the decimal multiplier
/// @param[out] unit unit
///
/// Prefixes:
/// \rst
///
/// Name | Symbol | Numerical value
/// ------ |--------|---------------
/// yotta | Y | 1e24
/// zetta | Z | 1e21
/// exa | E | 1e18
/// peta | P | 1e15
/// tera | T | 1e12
/// giga | G | 1e9
/// mega | M | 1e6
/// kilo | k | 1e3
/// hecto | h | 1e2
/// deca | da | 1e1
/// deci | d | 1e-1
/// centi | c | 1e-2
/// milli | m | 1e-3
/// micro | mu | 1e-6
/// nano | n | 1e-9
/// pico | p | 1e-12
/// femto | f | 1e-15
/// atto | a | 1e-18
/// zepto | z | 1e-21
/// yocto | y | 1e-24
/// ===== ====== ===============
/// Name Symbol Numerical value
/// ===== ====== ===============
/// yotta Y 1e24
/// zetta Z 1e21
/// exa E 1e18
/// peta P 1e15
/// tera T 1e12
/// giga G 1e9
/// mega M 1e6
/// kilo k 1e3
/// hecto h 1e2
/// deca da 1e1
/// deci d 1e-1
/// centi c 1e-2
/// milli m 1e-3
/// micro mu 1e-6
/// nano n 1e-9
/// pico p 1e-12
/// femto f 1e-15
/// atto a 1e-18
/// zepto z 1e-21
/// yocto y 1e-24
/// ===== ====== ===============
///
/// \endrst
///
/// [1]: 8th edition of the SI Brochure (2014), http://www.bipm.org/en/publications/si-brochure
Function ParseUnit(unitWithPrefix, prefix, numPrefix, unit)
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40 changes: 20 additions & 20 deletions Packages/MIES/MIES_Debugging.ipf
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Expand Up @@ -13,14 +13,14 @@ static StrConstant functionReturnMessage = "return value"
/// Debug function especially designed for usage in return statements.
///
/// For example calling the following function
///@code
///Function doStuff()
/// variable var = 1 + 2
/// return DEBUGPRINTv(var)
///End
///@endcode
/// @code
/// Function doStuff()
/// variable var = 1 + 2
/// return DEBUGPRINTv(var)
/// End
/// @endcode
/// will output
///@verbatim DEBUG doStuff(...)#L5: return value 3 @endverbatim
/// @verbatim DEBUG doStuff(...)#L5: return value 3 @endverbatim
/// to the history.
///
/// @hidecallgraph
Expand All @@ -46,14 +46,14 @@ End
/// Debug function especially designed for usage in return statements.
///
/// For example calling the following function
///@code
///Function/s doStuff()
/// variable str= "a" + "b"
/// return DEBUGPRINTs(str)
///End
///@endcode
/// @code
/// Function/s doStuff()
/// variable str= "a" + "b"
/// return DEBUGPRINTs(str)
/// End
/// @endcode
/// will output
///@verbatim DEBUG doStuff(...)#L5: return value ab @endverbatim
/// @verbatim DEBUG doStuff(...)#L5: return value ab @endverbatim
/// to the history.
///
/// @hidecallgraph
Expand All @@ -78,12 +78,12 @@ End
/// Outputs variables and strings with optional format argument.
///
///Examples:
///@code
///DEBUGPRINT("before a possible crash")
///DEBUGPRINT("some variable", var=myVariable)
///DEBUGPRINT("my string", str=myString)
///DEBUGPRINT("Current state", var=state, format="%.5f")
///@endcode
/// @code
/// DEBUGPRINT("before a possible crash")
/// DEBUGPRINT("some variable", var=myVariable)
/// DEBUGPRINT("my string", str=myString)
/// DEBUGPRINT("Current state", var=state, format="%.5f")
/// @endcode
///
/// @hidecallgraph
/// @hidecallergraph
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24 changes: 12 additions & 12 deletions Packages/MIES/MIES_GlobalStringAndVariableAccess.ipf
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Expand Up @@ -9,19 +9,19 @@
///
/// Instead if you have a global variable named `iceCreamCounter` in `root:myfood` you
/// would write in this file here a function like
///@code
///Function/S GetIceCreamCounterAsVariable()
/// return GetNVARAsString(createDFWithAllParents("root:myfood"), "iceCreamCounter")
///End
///@endcode
/// and then use it in your code as
///@code
///Function doStuff()
/// NVAR iceCreamCounter = $GetIceCreamCounterAsVariable()
/// @code
/// Function/S GetIceCreamCounterAsVariable()
/// return GetNVARAsString(createDFWithAllParents("root:myfood"), "iceCreamCounter")
/// End
/// @endcode
/// and then use it in your code as
/// @code
/// Function doStuff()
/// NVAR iceCreamCounter = $GetIceCreamCounterAsVariable()
///
/// iceCreamCounter += 1
///End
///@endcode
/// iceCreamCounter += 1
/// End
/// @endcode

/// @brief Returns the full path to a global variable
///
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74 changes: 39 additions & 35 deletions Packages/MIES/MIES_Utilities.ipf
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Expand Up @@ -50,11 +50,11 @@ End
/// @param errorMsg error message to output in failure case
///
/// Example usage:
///@code
///ControlInfo/W = $panelTitle popup_MoreSettings_DeviceType
///ASSERT(V_flag > 0, "Non-existing control or window")
///do something with S_value
///@endcode
/// @code
/// ControlInfo/W = $panelTitle popup_MoreSettings_DeviceType
/// ASSERT(V_flag > 0, "Non-existing control or window")
/// do something with S_value
/// @endcode
///
/// @hidecallgraph
/// @hidecallergraph
Expand Down Expand Up @@ -585,12 +585,12 @@ End
/// @brief Reset the debugger to the given state
///
/// Useful in conjunction with DisableDebugger() to temporarily disable the debugger
///@code
/// variable debuggerState = DisableDebugger()
/// // code which might trigger the debugger, e.g. CurveFit
/// ResetDebuggerState(debuggerState)
/// // now the debugger is in the same state as before
///@endcode
/// @code
/// variable debuggerState = DisableDebugger()
/// // code which might trigger the debugger, e.g. CurveFit
/// ResetDebuggerState(debuggerState)
/// // now the debugger is in the same state as before
/// @endcode
Function ResetDebuggerState(debuggerState)
variable debuggerState

Expand Down Expand Up @@ -1849,30 +1849,34 @@ End
/// @param[out] numPrefix numerical value of the decimal multiplier
/// @param[out] unit unit
///
/// Prefixes:
///
/// Name | Symbol | Numerical value
/// ------ |--------|---------------
/// yotta | Y | 1e24
/// zetta | Z | 1e21
/// exa | E | 1e18
/// peta | P | 1e15
/// tera | T | 1e12
/// giga | G | 1e9
/// mega | M | 1e6
/// kilo | k | 1e3
/// hecto | h | 1e2
/// deca | da | 1e1
/// deci | d | 1e-1
/// centi | c | 1e-2
/// milli | m | 1e-3
/// micro | mu | 1e-6
/// nano | n | 1e-9
/// pico | p | 1e-12
/// femto | f | 1e-15
/// atto | a | 1e-18
/// zepto | z | 1e-21
/// yocto | y | 1e-24
/// \rst
///
/// ===== ====== ===============
/// Name Symbol Numerical value
/// ===== ====== ===============
/// yotta Y 1e24
/// zetta Z 1e21
/// exa E 1e18
/// peta P 1e15
/// tera T 1e12
/// giga G 1e9
/// mega M 1e6
/// kilo k 1e3
/// hecto h 1e2
/// deca da 1e1
/// deci d 1e-1
/// centi c 1e-2
/// milli m 1e-3
/// micro mu 1e-6
/// nano n 1e-9
/// pico p 1e-12
/// femto f 1e-15
/// atto a 1e-18
/// zepto z 1e-21
/// yocto y 1e-24
/// ===== ====== ===============
///
/// \endrst
///
/// [1]: 8th edition of the SI Brochure (2014), http://www.bipm.org/en/publications/si-brochure
Function ParseUnit(unitWithPrefix, prefix, numPrefix, unit)
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43 changes: 24 additions & 19 deletions Packages/MIES/MIES_WaveDataFolderGetters.ipf
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Expand Up @@ -3925,25 +3925,30 @@ End
/// - Column specific GUI control settings usually associated with control name number
///
/// Columns:
/// - DACs
/// 0: HSState State of control Check_DataAcqHS_RowNum. 0 = UnChecked, 1 = Checked
/// 1: HSMode Clamp mode of HS number that matches Row number. 0 = VC, 1 = IC, 2 = NC.
/// 2: DAState State of control Check_DA_RowNum. 0 = UnChecked, 1 = Checked
/// 3: DAGain Internal number stored in control Gain_DA_RowNum. Gain is user/hardware defined.
/// 4: DAScale Internal number stored in setvar:Scale_DA_RowNum. Scalar is user defined.
/// 5: DAStartIndex PopupMenu Index of popupMenu:Wave_DA_RowNum. Stores index of active DA stimulus set during data acquisition. Stores index of next DA stimulus set when data acquistion is not active.
/// 6: DAEndIndex PopupMenu Index of popupMenu:IndexEnd_DA_RowNum. Stores the index of the last DA stimulus set used in indexed aquisition mode.
/// 7: ADState State of checkbox control Check_AD_RowNum. 0 = UnChecked, 1 = Checked
/// 8: ADGain Internal number stored in Gain_AD_RowNum. Gain is user/hardware defined.
/// 9: TTLState State of checkbox control Check_TTL_RowNum. 0 = UnChecked, 1 = Checked
/// 10: TTLStartIndex PopupMenu Index of popupMenu:Wave_TTL_RowNum. Stores index of active TTL stimulus set during data acquisition. Stores index of next TTL stimulus set when data acquistion is not active.
/// 11: TTLEndIndex PopupMenu Index of popupMenu:IndexEnd_TTL_RowNum. Stores the index of the last TTL stimulus set used in indexed aquisition mode.
/// 12: AsyncState State of control Check_AsyncAD_RowNum. 0 = UnChecked, 1 = Checked
/// 13: AsyncGain Internal number stored in control SetVar_AsyncAD_Gain_RowNum. Gain is user/hardware defined.
/// 14: AlarmState State of control check_AsyncAlarm_RowNum. 0 = UnChecked, 1 = Checked
/// 15: AlarmMin Internal number stored in control min_AsyncAD__RowNum. The minium value alarm trigger.
/// 16: AlarmMax Internal number stored in control max_AsyncAD_RowNum. The max value alarm trigger.
/// 17+: Unique controls
/// - 0: HSState State of control Check_DataAcqHS_RowNum. 0 = UnChecked, 1 = Checked
/// - 1: HSMode Clamp mode of HS number that matches Row number. 0 = VC, 1 = IC, 2 = NC.
/// - 2: DAState State of control Check_DA_RowNum. 0 = UnChecked, 1 = Checked
/// - 3: DAGain Internal number stored in control Gain_DA_RowNum. Gain is user/hardware defined.
/// - 4: DAScale Internal number stored in setvar:Scale_DA_RowNum. Scalar is user defined.
/// - 5: DAStartIndex PopupMenu Index of popupMenu:Wave_DA_RowNum. Stores index
/// of active DA stimulus set during data acquisition. Stores index of next DA
/// stimulus set when data acquistion is not active.
/// - 6: DAEndIndex PopupMenu Index of popupMenu:IndexEnd_DA_RowNum. Stores the
/// index of the last DA stimulus set used in indexed aquisition mode.
/// - 7: ADState State of checkbox control Check_AD_RowNum. 0 = UnChecked, 1 = Checked
/// - 8: ADGain Internal number stored in Gain_AD_RowNum. Gain is user/hardware defined.
/// - 9: TTLState State of checkbox control Check_TTL_RowNum. 0 = UnChecked, 1 = Checked
/// - 10: TTLStartIndex PopupMenu Index of popupMenu:Wave_TTL_RowNum. Stores
/// index of active TTL stimulus set during data acquisition. Stores index of
/// next TTL stimulus set when data acquistion is not active.
/// - 11: TTLEndIndex PopupMenu Index of popupMenu:IndexEnd_TTL_RowNum. Stores
/// the index of the last TTL stimulus set used in indexed aquisition mode.
/// - 12: AsyncState State of control Check_AsyncAD_RowNum. 0 = UnChecked, 1 = Checked
/// - 13: AsyncGain Internal number stored in control SetVar_AsyncAD_Gain_RowNum. Gain is user/hardware defined.
/// - 14: AlarmState State of control check_AsyncAlarm_RowNum. 0 = UnChecked, 1 = Checked
/// - 15: AlarmMin Internal number stored in control min_AsyncAD__RowNum. The minium value alarm trigger.
/// - 16: AlarmMax Internal number stored in control max_AsyncAD_RowNum. The max value alarm trigger.
/// - 17+: Unique controls
Function/Wave GetDA_EphysGuiStateNum(panelTitle)
string panelTitle

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10 changes: 9 additions & 1 deletion Packages/doc/.gitignore
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@@ -1,4 +1,12 @@

# Doxygen Build
html
latex
xml
releasenotes.rst
readme.rst
file
filelist.rst
struct
structlist.rst
namespace
namespacelist.rst
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