From 80eb485e7b5c0ec3ba2de35698fc4e3a4244451e Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 15:22:31 +1200 Subject: [PATCH 1/9] Structure of chapter 3 (take 1) --- ...ecC06_interpretation_of_initial_values.rst | 7 ------ .../specC07_effect_of_units_on_variables.rst | 7 ------ ...pecC09_interpretation_of_encapsulation.rst | 7 ------ ...pecC10_interpretation_of_map_variables.rst | 7 ------ .../specC_components.rst | 17 +++++++++++++ ...ation_of_imports.rst => specC_imports.rst} | 1 - ...ion_of_mathematics.rst => specC_maths.rst} | 6 +++++ .../formal_and_informative/specC_models.rst | 19 +++++++++++++++ ...f_variable_resets.rst => specC_resets.rst} | 1 - ...pretation_of_units.rst => specC_units.rst} | 11 ++++++++- .../specC_variables.rst | 24 +++++++++++++++++++ src/reference/index_sectionC.rst | 10 ++++++-- 12 files changed, 84 insertions(+), 33 deletions(-) delete mode 100644 src/reference/formal_and_informative/specC06_interpretation_of_initial_values.rst delete mode 100644 src/reference/formal_and_informative/specC07_effect_of_units_on_variables.rst delete mode 100644 src/reference/formal_and_informative/specC09_interpretation_of_encapsulation.rst delete mode 100644 src/reference/formal_and_informative/specC10_interpretation_of_map_variables.rst create mode 100644 src/reference/formal_and_informative/specC_components.rst rename src/reference/formal_and_informative/{specC01_interpretation_of_imports.rst => specC_imports.rst} (93%) rename src/reference/formal_and_informative/{specC08_interpretation_of_mathematics.rst => specC_maths.rst} (50%) create mode 100644 src/reference/formal_and_informative/specC_models.rst rename src/reference/formal_and_informative/{specC11_interpretation_of_variable_resets.rst => specC_resets.rst} (94%) rename src/reference/formal_and_informative/{specC03_interpretation_of_units.rst => specC_units.rst} (62%) create mode 100644 src/reference/formal_and_informative/specC_variables.rst diff --git a/src/reference/formal_and_informative/specC06_interpretation_of_initial_values.rst b/src/reference/formal_and_informative/specC06_interpretation_of_initial_values.rst deleted file mode 100644 index 5b7d960d..00000000 --- a/src/reference/formal_and_informative/specC06_interpretation_of_initial_values.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _specC06: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_interpretation_of_initial_values_start - :end-before: marker_interpretation_of_initial_values_end - -.. include:: ../informative/informC06_interpretation_of_initial_values.rst diff --git a/src/reference/formal_and_informative/specC07_effect_of_units_on_variables.rst b/src/reference/formal_and_informative/specC07_effect_of_units_on_variables.rst deleted file mode 100644 index e3469932..00000000 --- a/src/reference/formal_and_informative/specC07_effect_of_units_on_variables.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _specC07: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_effect_of_units_on_variables_start - :end-before: marker_effect_of_units_on_variables_end - -.. todo ../informative/informC07_effect_of_units_on_variables.rst diff --git a/src/reference/formal_and_informative/specC09_interpretation_of_encapsulation.rst b/src/reference/formal_and_informative/specC09_interpretation_of_encapsulation.rst deleted file mode 100644 index f9c4212c..00000000 --- a/src/reference/formal_and_informative/specC09_interpretation_of_encapsulation.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _specC09: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_interpretation_of_encapsulation_start - :end-before: marker_interpretation_of_encapsulation_end - -.. todo ../informative/informC09_interpretation_of_encapsulation.rst diff --git a/src/reference/formal_and_informative/specC10_interpretation_of_map_variables.rst b/src/reference/formal_and_informative/specC10_interpretation_of_map_variables.rst deleted file mode 100644 index f46605cd..00000000 --- a/src/reference/formal_and_informative/specC10_interpretation_of_map_variables.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _specC10: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_interpretation_of_map_variables_start - :end-before: marker_interpretation_of_map_variables_end - -.. todo ../informative/informC10_interpretation_of_map_variables.rst diff --git a/src/reference/formal_and_informative/specC_components.rst b/src/reference/formal_and_informative/specC_components.rst new file mode 100644 index 00000000..fe0057d0 --- /dev/null +++ b/src/reference/formal_and_informative/specC_components.rst @@ -0,0 +1,17 @@ +.. note:: + + A component is a conceptual entity representing a group of variables. + + A component is defined by a :code:component element or an :code:import component element. + + A component has a name, determined by the :code:name attribute of its :code:component element or :code:import component element. + + A component contains zero or more variables [LINK **TODO**]. + + A component contains zero or more encapsulated components, as defined in section ABC **TODO**. + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_interpretation_of_encapsulation_start + :end-before: marker_interpretation_of_encapsulation_end + +.. todo ../informative/informC09_interpretation_of_encapsulation.rst diff --git a/src/reference/formal_and_informative/specC01_interpretation_of_imports.rst b/src/reference/formal_and_informative/specC_imports.rst similarity index 93% rename from src/reference/formal_and_informative/specC01_interpretation_of_imports.rst rename to src/reference/formal_and_informative/specC_imports.rst index da43814e..e2353f0b 100644 --- a/src/reference/formal_and_informative/specC01_interpretation_of_imports.rst +++ b/src/reference/formal_and_informative/specC_imports.rst @@ -1,4 +1,3 @@ -.. _specC01: .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_imports_start diff --git a/src/reference/formal_and_informative/specC08_interpretation_of_mathematics.rst b/src/reference/formal_and_informative/specC_maths.rst similarity index 50% rename from src/reference/formal_and_informative/specC08_interpretation_of_mathematics.rst rename to src/reference/formal_and_informative/specC_maths.rst index 886594dd..b4680fb1 100644 --- a/src/reference/formal_and_informative/specC08_interpretation_of_mathematics.rst +++ b/src/reference/formal_and_informative/specC_maths.rst @@ -5,3 +5,9 @@ :end-before: marker_interpretation_of_mathematics_end .. todo ../informative/informC08_interpretation_of_mathematics.rst + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_interpretation_of_initial_values_start + :end-before: marker_interpretation_of_initial_values_end + +.. include:: ../informative/informC06_interpretation_of_initial_values.rst \ No newline at end of file diff --git a/src/reference/formal_and_informative/specC_models.rst b/src/reference/formal_and_informative/specC_models.rst new file mode 100644 index 00000000..efecdf83 --- /dev/null +++ b/src/reference/formal_and_informative/specC_models.rst @@ -0,0 +1,19 @@ + + +.. note:: + + A *model* is a conceptual entity defining a system of equations. + + A model is defined by a :code:`model` element. + + A model has a name, determined by the :code:`name` attribute of its :code:`model` element. + + A model contains zero or more units [LINK **TODO**]. + + A model contains zero or more components [LINK **TODO**]. + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_interpretation_of_models_start + :end-before: marker_interpretation_of_models_end + +.. todo ../informative/informC_model.rst diff --git a/src/reference/formal_and_informative/specC11_interpretation_of_variable_resets.rst b/src/reference/formal_and_informative/specC_resets.rst similarity index 94% rename from src/reference/formal_and_informative/specC11_interpretation_of_variable_resets.rst rename to src/reference/formal_and_informative/specC_resets.rst index dbfcf84a..b9fd7870 100644 --- a/src/reference/formal_and_informative/specC11_interpretation_of_variable_resets.rst +++ b/src/reference/formal_and_informative/specC_resets.rst @@ -1,4 +1,3 @@ -.. _specC11: .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_variable_resets_start diff --git a/src/reference/formal_and_informative/specC03_interpretation_of_units.rst b/src/reference/formal_and_informative/specC_units.rst similarity index 62% rename from src/reference/formal_and_informative/specC03_interpretation_of_units.rst rename to src/reference/formal_and_informative/specC_units.rst index a545498a..52d5be6e 100644 --- a/src/reference/formal_and_informative/specC03_interpretation_of_units.rst +++ b/src/reference/formal_and_informative/specC_units.rst @@ -1,4 +1,13 @@ -.. _specC03: + +.. note:: + + A units definition is a conceptual entity representing physical units. + + A units definition is defined by a :code:`units` element or an `:code:import units` element, or is one of the predefined units of table X. + + A units definition has a name, determined by the :code:`name` attribute of its :code:units element or :code:import units element, or by the "Name" column in table X for predefined units. + + A units definition has a unit reduction, determined by the **TODO** rules in section XYZ. .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_units_start diff --git a/src/reference/formal_and_informative/specC_variables.rst b/src/reference/formal_and_informative/specC_variables.rst new file mode 100644 index 00000000..b3de3698 --- /dev/null +++ b/src/reference/formal_and_informative/specC_variables.rst @@ -0,0 +1,24 @@ +.. note:: + + A *variable* is a conceptual entity representing a mathematical variable. + + A variable is defined by a :code:`variable` element. + + A variable has a *name*, determined by the :code:`name` attribute of its :code:`variable` element. + + A variable has *units*, determined by the :code:`units` attribute of its :code:`variable` element. + The value of the :code:`units` attribute of a :code:`variable` element must equal the name of a predefined unit, or a unit defined within the model. + + A variable has an *initial value*, determined by the :code:`initial_value` attribute of its :code:`variable`. + + A variable has an *interface*, determined by the :code:`interface` attribute of its :code:`variable` element. + + A variable can be part of an *equivalent variable network*, as defined in section PQR **TODO**. + + A variable can be used in equations, see section KLM **TODO**. + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_interpretation_of_map_variables_start + :end-before: marker_interpretation_of_map_variables_end + +.. todo ../informative/informC10_interpretation_of_map_variables.rst diff --git a/src/reference/index_sectionC.rst b/src/reference/index_sectionC.rst index 8f5dae6c..a23d98ae 100644 --- a/src/reference/index_sectionC.rst +++ b/src/reference/index_sectionC.rst @@ -6,6 +6,12 @@ Interpretation .. toctree:: :maxdepth: 1 - :glob: - formal_and_informative/specC* + formal_and_informative/specC_models.rst + formal_and_informative/specC_units.rst + formal_and_informative/specC_components.rst + formal_and_informative/specC_variables.rst + formal_and_informative/specC_imports.rst + formal_and_informative/specC_maths.rst + formal_and_informative/specC_resets.rst + From 83c40ffc2d322288b2a5c2bcfd9b7284d05380e1 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 15:32:43 +1200 Subject: [PATCH 2/9] Basic placeholders for preamble, css --- .../formal_and_informative/specC_components.rst | 8 ++++---- .../formal_and_informative/specC_imports.rst | 4 ++++ .../formal_and_informative/specC_maths.rst | 5 ++++- .../formal_and_informative/specC_models.rst | 3 +-- .../formal_and_informative/specC_resets.rst | 4 ++++ .../formal_and_informative/specC_units.rst | 10 +++++----- .../formal_and_informative/specC_variables.rst | 2 +- src/static/css/cellml.css | 14 ++++++++++++++ 8 files changed, 37 insertions(+), 13 deletions(-) diff --git a/src/reference/formal_and_informative/specC_components.rst b/src/reference/formal_and_informative/specC_components.rst index fe0057d0..0e02c98b 100644 --- a/src/reference/formal_and_informative/specC_components.rst +++ b/src/reference/formal_and_informative/specC_components.rst @@ -1,10 +1,10 @@ -.. note:: +.. container:: preamble - A component is a conceptual entity representing a group of variables. + A *component* is a conceptual entity representing a group of variables. - A component is defined by a :code:component element or an :code:import component element. + A component is defined by a :code:`component` element or an :code:`import component` element. - A component has a name, determined by the :code:name attribute of its :code:component element or :code:import component element. + A component has a *name*, determined by the :code:`name` attribute of its :code:`component` element or :code:`import component` element. A component contains zero or more variables [LINK **TODO**]. diff --git a/src/reference/formal_and_informative/specC_imports.rst b/src/reference/formal_and_informative/specC_imports.rst index e2353f0b..801cd09f 100644 --- a/src/reference/formal_and_informative/specC_imports.rst +++ b/src/reference/formal_and_informative/specC_imports.rst @@ -1,4 +1,8 @@ +.. container:: preamble + + **TODO** Preamble for imports goes here + .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_imports_start :end-before: marker_interpretation_of_imports_end diff --git a/src/reference/formal_and_informative/specC_maths.rst b/src/reference/formal_and_informative/specC_maths.rst index b4680fb1..ca310af1 100644 --- a/src/reference/formal_and_informative/specC_maths.rst +++ b/src/reference/formal_and_informative/specC_maths.rst @@ -1,4 +1,7 @@ -.. _specC08: + +.. container:: preamble + + **TODO** Preamble for maths goes here .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_mathematics_start diff --git a/src/reference/formal_and_informative/specC_models.rst b/src/reference/formal_and_informative/specC_models.rst index efecdf83..a08aed8e 100644 --- a/src/reference/formal_and_informative/specC_models.rst +++ b/src/reference/formal_and_informative/specC_models.rst @@ -1,6 +1,5 @@ - -.. note:: +.. container:: preamble A *model* is a conceptual entity defining a system of equations. diff --git a/src/reference/formal_and_informative/specC_resets.rst b/src/reference/formal_and_informative/specC_resets.rst index b9fd7870..be01005c 100644 --- a/src/reference/formal_and_informative/specC_resets.rst +++ b/src/reference/formal_and_informative/specC_resets.rst @@ -1,4 +1,8 @@ +.. container:: preamble + + **TODO** Preamble for resets goes here + .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_variable_resets_start :end-before: marker_interpretation_of_variable_resets_end diff --git a/src/reference/formal_and_informative/specC_units.rst b/src/reference/formal_and_informative/specC_units.rst index 52d5be6e..04840fe8 100644 --- a/src/reference/formal_and_informative/specC_units.rst +++ b/src/reference/formal_and_informative/specC_units.rst @@ -1,13 +1,13 @@ -.. note:: +.. container:: preamble - A units definition is a conceptual entity representing physical units. + A *units definition* is a conceptual entity representing physical units. - A units definition is defined by a :code:`units` element or an `:code:import units` element, or is one of the predefined units of table X. + A units definition is defined by a :code:`units` element or an :code:`import units` element, or is one of the built-in units listed in the :ref:`Built-in Units table`. - A units definition has a name, determined by the :code:`name` attribute of its :code:units element or :code:import units element, or by the "Name" column in table X for predefined units. + A units definition has a *name*, determined by the :code:`name` attribute of its :code:`units` element or :code:`import units` element, or by the "Name" column in the :ref:`Built-in Units table`. - A units definition has a unit reduction, determined by the **TODO** rules in section XYZ. + A units definition has a *unit reduction*, determined by the rules in section XYZ **TODO**. .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_units_start diff --git a/src/reference/formal_and_informative/specC_variables.rst b/src/reference/formal_and_informative/specC_variables.rst index b3de3698..63890f8c 100644 --- a/src/reference/formal_and_informative/specC_variables.rst +++ b/src/reference/formal_and_informative/specC_variables.rst @@ -1,4 +1,4 @@ -.. note:: +.. container:: preamble A *variable* is a conceptual entity representing a mathematical variable. diff --git a/src/static/css/cellml.css b/src/static/css/cellml.css index b4ac4bfb..471ce900 100644 --- a/src/static/css/cellml.css +++ b/src/static/css/cellml.css @@ -83,6 +83,20 @@ li { content: " -"; } +.preamble { + background: rgb(242, 249, 227); + padding: 10px; + + margin-top: 0; + margin-bottom: 15px; + margin-left: 0; + margin-right: 0; + + line-height: 24px; + font-family: "Lato", "proxima-nova", "Helvetica Neue", "Arial", sans-serif; +} + + .infospec { /* border-top: 1px solid #b9c6dd; */ background: #e1eaf0; From e79880bc889973c83320f40224c4a053f8a6b617 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 15:43:29 +1200 Subject: [PATCH 3/9] Added interpretation of models section to chapter 3 source --- src/reference/sectionC_interpretation.inc | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/reference/sectionC_interpretation.inc b/src/reference/sectionC_interpretation.inc index 3515890f..3f251c50 100644 --- a/src/reference/sectionC_interpretation.inc +++ b/src/reference/sectionC_interpretation.inc @@ -1,5 +1,16 @@ .. _sectionC: + +.. marker_interpretation_of_models_start + +Interpretation of ``model`` elements +------------------------------------ + +**TODO** Stuff about models should go here! + +.. marker_interpretation_of_models_end + + .. marker_interpretation_of_imports_start .. _specC_interpretation_of_imports: From 0f15c8413890f841cb9d6dd2c88ccf6dbf48e7a6 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 15:45:23 +1200 Subject: [PATCH 4/9] testing order ... WIP --- .../formal_and_informative/specC_models.rst | 12 ------------ src/reference/sectionC_interpretation.inc | 13 +++++++++++++ 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/src/reference/formal_and_informative/specC_models.rst b/src/reference/formal_and_informative/specC_models.rst index a08aed8e..4fc802b8 100644 --- a/src/reference/formal_and_informative/specC_models.rst +++ b/src/reference/formal_and_informative/specC_models.rst @@ -1,16 +1,4 @@ -.. container:: preamble - - A *model* is a conceptual entity defining a system of equations. - - A model is defined by a :code:`model` element. - - A model has a name, determined by the :code:`name` attribute of its :code:`model` element. - - A model contains zero or more units [LINK **TODO**]. - - A model contains zero or more components [LINK **TODO**]. - .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_models_start :end-before: marker_interpretation_of_models_end diff --git a/src/reference/sectionC_interpretation.inc b/src/reference/sectionC_interpretation.inc index 3f251c50..ac157065 100644 --- a/src/reference/sectionC_interpretation.inc +++ b/src/reference/sectionC_interpretation.inc @@ -6,6 +6,19 @@ Interpretation of ``model`` elements ------------------------------------ +.. container:: preamble + + A *model* is a conceptual entity defining a system of equations. + + A model is defined by a :code:`model` element. + + A model has a name, determined by the :code:`name` attribute of its :code:`model` element. + + A model contains zero or more units [LINK **TODO**]. + + A model contains zero or more components [LINK **TODO**]. + + **TODO** Stuff about models should go here! .. marker_interpretation_of_models_end From c1cfc55d68eedd2a3cbe1fed411ecd404a5f8528 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 15:52:14 +1200 Subject: [PATCH 5/9] moved preamble into sectionC source --- .../specC_components.rst | 11 ---- .../formal_and_informative/specC_imports.rst | 4 -- .../formal_and_informative/specC_maths.rst | 4 -- .../formal_and_informative/specC_resets.rst | 4 -- .../formal_and_informative/specC_units.rst | 10 --- .../specC_variables.rst | 18 ------ src/reference/sectionC_interpretation.inc | 63 ++++++++++++++++++- 7 files changed, 60 insertions(+), 54 deletions(-) diff --git a/src/reference/formal_and_informative/specC_components.rst b/src/reference/formal_and_informative/specC_components.rst index 0e02c98b..2697d574 100644 --- a/src/reference/formal_and_informative/specC_components.rst +++ b/src/reference/formal_and_informative/specC_components.rst @@ -1,14 +1,3 @@ -.. container:: preamble - - A *component* is a conceptual entity representing a group of variables. - - A component is defined by a :code:`component` element or an :code:`import component` element. - - A component has a *name*, determined by the :code:`name` attribute of its :code:`component` element or :code:`import component` element. - - A component contains zero or more variables [LINK **TODO**]. - - A component contains zero or more encapsulated components, as defined in section ABC **TODO**. .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_encapsulation_start diff --git a/src/reference/formal_and_informative/specC_imports.rst b/src/reference/formal_and_informative/specC_imports.rst index 801cd09f..e2353f0b 100644 --- a/src/reference/formal_and_informative/specC_imports.rst +++ b/src/reference/formal_and_informative/specC_imports.rst @@ -1,8 +1,4 @@ -.. container:: preamble - - **TODO** Preamble for imports goes here - .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_imports_start :end-before: marker_interpretation_of_imports_end diff --git a/src/reference/formal_and_informative/specC_maths.rst b/src/reference/formal_and_informative/specC_maths.rst index ca310af1..1ff6e29a 100644 --- a/src/reference/formal_and_informative/specC_maths.rst +++ b/src/reference/formal_and_informative/specC_maths.rst @@ -1,8 +1,4 @@ -.. container:: preamble - - **TODO** Preamble for maths goes here - .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_mathematics_start :end-before: marker_interpretation_of_mathematics_end diff --git a/src/reference/formal_and_informative/specC_resets.rst b/src/reference/formal_and_informative/specC_resets.rst index be01005c..b9fd7870 100644 --- a/src/reference/formal_and_informative/specC_resets.rst +++ b/src/reference/formal_and_informative/specC_resets.rst @@ -1,8 +1,4 @@ -.. container:: preamble - - **TODO** Preamble for resets goes here - .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_variable_resets_start :end-before: marker_interpretation_of_variable_resets_end diff --git a/src/reference/formal_and_informative/specC_units.rst b/src/reference/formal_and_informative/specC_units.rst index 04840fe8..b6cb8a96 100644 --- a/src/reference/formal_and_informative/specC_units.rst +++ b/src/reference/formal_and_informative/specC_units.rst @@ -1,14 +1,4 @@ -.. container:: preamble - - A *units definition* is a conceptual entity representing physical units. - - A units definition is defined by a :code:`units` element or an :code:`import units` element, or is one of the built-in units listed in the :ref:`Built-in Units table`. - - A units definition has a *name*, determined by the :code:`name` attribute of its :code:`units` element or :code:`import units` element, or by the "Name" column in the :ref:`Built-in Units table`. - - A units definition has a *unit reduction*, determined by the rules in section XYZ **TODO**. - .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_units_start :end-before: marker_interpretation_of_units_1 diff --git a/src/reference/formal_and_informative/specC_variables.rst b/src/reference/formal_and_informative/specC_variables.rst index 63890f8c..f20f6163 100644 --- a/src/reference/formal_and_informative/specC_variables.rst +++ b/src/reference/formal_and_informative/specC_variables.rst @@ -1,21 +1,3 @@ -.. container:: preamble - - A *variable* is a conceptual entity representing a mathematical variable. - - A variable is defined by a :code:`variable` element. - - A variable has a *name*, determined by the :code:`name` attribute of its :code:`variable` element. - - A variable has *units*, determined by the :code:`units` attribute of its :code:`variable` element. - The value of the :code:`units` attribute of a :code:`variable` element must equal the name of a predefined unit, or a unit defined within the model. - - A variable has an *initial value*, determined by the :code:`initial_value` attribute of its :code:`variable`. - - A variable has an *interface*, determined by the :code:`interface` attribute of its :code:`variable` element. - - A variable can be part of an *equivalent variable network*, as defined in section PQR **TODO**. - - A variable can be used in equations, see section KLM **TODO**. .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_map_variables_start diff --git a/src/reference/sectionC_interpretation.inc b/src/reference/sectionC_interpretation.inc index ac157065..940a08e5 100644 --- a/src/reference/sectionC_interpretation.inc +++ b/src/reference/sectionC_interpretation.inc @@ -18,7 +18,7 @@ Interpretation of ``model`` elements A model contains zero or more components [LINK **TODO**]. - + **TODO** Stuff about models should go here! .. marker_interpretation_of_models_end @@ -31,6 +31,10 @@ Interpretation of ``model`` elements Interpretation of ``import`` elements ------------------------------------- +.. container:: preamble + + **TODO** Preamble for imports goes here + #. Each :code:`import` element present in a :ref:`CellML infoset` (the importing infoset) SHALL define a new and distinct instance of the CellML infoset which is referenced by the :code:`href` attribute (the imported infoset). This imported infoset instance SHALL provide the context in which the child of an import element (a :code:`units` or :code:`component` element) is defined and interpreted. @@ -156,6 +160,18 @@ The term "units reference" refers to the value of a :code:`units_ref` attribute Interpretation of ``units`` elements ------------------------------------ +.. container:: preamble + + A *units definition* is a conceptual entity representing physical units. + + A units definition is defined by a :code:`units` element or an :code:`import units` element, or is one of the built-in units listed in the :ref:`Built-in Units table`. + + A units definition has a *name*, determined by the :code:`name` attribute of its :code:`units` element or :code:`import units` element, or by the "Name" column in the :ref:`Built-in Units table`. + + A units definition has a *unit reduction*, determined by the rules in section XYZ **TODO**. + + + 1. The :code:`units` element SHALL be interpreted as the product of its :code:`unit` element children, according to the following rules: @@ -313,6 +329,11 @@ Effect of ``units`` on a ``variable`` Interpretation of ``math`` elements ----------------------------------- +.. container:: preamble + + **TODO** Preamble for maths and initial values goes here + + #. The following :code:`component` elements SHALL, for the purposes of this specification, be "pertinent component elements": #. All :code:`component` elements in the top-level :ref:`CellML infoset` for the :ref:`CellML model`; @@ -330,10 +351,22 @@ Interpretation of ``math`` elements .. _specC_interpretation_of_encapsulation: - Interpretation of ``encapsulation`` elements -------------------------------------------- +.. container:: preamble + + A *component* is a conceptual entity representing a group of variables. + + A component is defined by a :code:`component` element or an :code:`import component` element. + + A component has a *name*, determined by the :code:`name` attribute of its :code:`component` element or :code:`import component` element. + + A component contains zero or more variables [LINK **TODO**]. + + A component contains zero or more encapsulated components, as defined in section ABC **TODO**. + + #. For the purposes of this specification, there SHALL be a "conceptual encapsulation digraph" in which there is EXACTLY one node for every component in the :ref:`CellML model`. Therefore the encapsulation digraph will not contain any loops. @@ -360,6 +393,26 @@ Interpretation of ``encapsulation`` elements Interpretation of ``map_variables`` elements -------------------------------------------- +.. container:: preamble + + A *variable* is a conceptual entity representing a mathematical variable. + + A variable is defined by a :code:`variable` element. + + A variable has a *name*, determined by the :code:`name` attribute of its :code:`variable` element. + + A variable has *units*, determined by the :code:`units` attribute of its :code:`variable` element. + The value of the :code:`units` attribute of a :code:`variable` element must equal the name of a predefined unit, or a unit defined within the model. + + A variable has an *initial value*, determined by the :code:`initial_value` attribute of its :code:`variable`. + + A variable has an *interface*, determined by the :code:`interface` attribute of its :code:`variable` element. + + A variable can be part of an *equivalent variable network*, as defined in section PQR **TODO**. + + A variable can be used in equations, see section KLM **TODO**. + + #. For the purposes of this specification, the variable equivalence (conceptual) network SHALL be an undirected graph with one node for every :code:`variable` element in the :ref:`CellML model`. The arcs of this graph SHALL be equivalences defined in the CellML model. @@ -416,10 +469,14 @@ Interpretation of ``map_variables`` elements .. _specC_interpretation_of_variable_resets: - Interpretation of ``reset`` elements ------------------------------------ +.. container:: preamble + + **TODO** Preamble for resets goes here + + #. Each :code:`reset` element describes a change to be applied to the variable referenced by the :code:`variable` attribute when specified conditions are met during the simulation of the model. #. All :code:`reset` elements SHALL be considered sequentially for the connected variable set (see :ref:`Interpretation of map_variables`) to which the referenced variable belongs. From 2c471d50672ac0715112a37a47c778ca5b660215 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 16:00:37 +1200 Subject: [PATCH 6/9] Update cellml.css --- src/static/css/cellml.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/static/css/cellml.css b/src/static/css/cellml.css index 471ce900..4a7a7cd9 100644 --- a/src/static/css/cellml.css +++ b/src/static/css/cellml.css @@ -96,6 +96,10 @@ li { font-family: "Lato", "proxima-nova", "Helvetica Neue", "Arial", sans-serif; } +.preamble > p{ + margin-bottom: 0; +} + .infospec { /* border-top: 1px solid #b9c6dd; */ From 6c3e53d9033eef6ab2ae614728ae4471939aaa61 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 16:02:09 +1200 Subject: [PATCH 7/9] Update cellml.css --- src/static/css/cellml.css | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/src/static/css/cellml.css b/src/static/css/cellml.css index 4a7a7cd9..fcb2ff8d 100644 --- a/src/static/css/cellml.css +++ b/src/static/css/cellml.css @@ -84,7 +84,8 @@ li { } .preamble { - background: rgb(242, 249, 227); + background: #ececec; + color: saddlebrown; padding: 10px; margin-top: 0; @@ -96,7 +97,7 @@ li { font-family: "Lato", "proxima-nova", "Helvetica Neue", "Arial", sans-serif; } -.preamble > p{ +.preamble > p { margin-bottom: 0; } From 8015d0920b6cf79c0b6fc2d0be135c6a0324450b Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 16:04:58 +1200 Subject: [PATCH 8/9] Update cellml.css --- src/static/css/cellml.css | 5 ----- 1 file changed, 5 deletions(-) diff --git a/src/static/css/cellml.css b/src/static/css/cellml.css index fcb2ff8d..2d4c4fc9 100644 --- a/src/static/css/cellml.css +++ b/src/static/css/cellml.css @@ -97,11 +97,6 @@ li { font-family: "Lato", "proxima-nova", "Helvetica Neue", "Arial", sans-serif; } -.preamble > p { - margin-bottom: 0; -} - - .infospec { /* border-top: 1px solid #b9c6dd; */ background: #e1eaf0; From 61a8c1d4f186675eb13a17f55c87f98e81f19d10 Mon Sep 17 00:00:00 2001 From: Keri Moyle Date: Wed, 15 Apr 2020 20:01:36 +1200 Subject: [PATCH 9/9] Including placeholders for everything --- .../specC02_units_reference.rst | 11 ----------- .../specC04_component_reference.rst | 7 ------- .../specC05_variable_reference.rst | 7 ------- .../formal_and_informative/specC_components.rst | 10 ++++++++++ src/reference/formal_and_informative/specC_units.rst | 12 +++++++++++- .../formal_and_informative/specC_variables.rst | 10 ++++++++++ 6 files changed, 31 insertions(+), 26 deletions(-) delete mode 100644 src/reference/formal_and_informative/specC02_units_reference.rst delete mode 100644 src/reference/formal_and_informative/specC04_component_reference.rst delete mode 100644 src/reference/formal_and_informative/specC05_variable_reference.rst diff --git a/src/reference/formal_and_informative/specC02_units_reference.rst b/src/reference/formal_and_informative/specC02_units_reference.rst deleted file mode 100644 index 41cb8017..00000000 --- a/src/reference/formal_and_informative/specC02_units_reference.rst +++ /dev/null @@ -1,11 +0,0 @@ -.. _specC02: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_units_reference_start - :end-before: marker_units_reference1 - -.. include:: ../informative/informC02_units_reference.rst - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_units_reference1 - :end-before: marker_units_reference_end diff --git a/src/reference/formal_and_informative/specC04_component_reference.rst b/src/reference/formal_and_informative/specC04_component_reference.rst deleted file mode 100644 index 9bd86a09..00000000 --- a/src/reference/formal_and_informative/specC04_component_reference.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _specC04: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_component_reference_start - :end-before: marker_component_reference_end - -.. include:: ../informative/informC04_component_reference.rst diff --git a/src/reference/formal_and_informative/specC05_variable_reference.rst b/src/reference/formal_and_informative/specC05_variable_reference.rst deleted file mode 100644 index c7a4388f..00000000 --- a/src/reference/formal_and_informative/specC05_variable_reference.rst +++ /dev/null @@ -1,7 +0,0 @@ -.. _specC05: - -.. include:: ../sectionC_interpretation.inc - :start-after: marker_variable_reference_start - :end-before: marker_variable_reference_end - -.. include:: ../informative/informC05_variable_reference.rst diff --git a/src/reference/formal_and_informative/specC_components.rst b/src/reference/formal_and_informative/specC_components.rst index 5e14f27f..752cdd0c 100644 --- a/src/reference/formal_and_informative/specC_components.rst +++ b/src/reference/formal_and_informative/specC_components.rst @@ -1,4 +1,14 @@ +.. ** PREVIOUSLY THIS WAS THE COMPONENT_REFERENCE SECTION ** + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_component_reference_start + :end-before: marker_component_reference_end + +.. include:: ../informative/informC04_component_reference.rst + +.. ** PREVIOUSLY THIS WAS THE INTERPRETATION OF ENCAPSULATIONS ** + .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_encapsulation_start :end-before: marker_interpretation_of_encapsulation_1 diff --git a/src/reference/formal_and_informative/specC_units.rst b/src/reference/formal_and_informative/specC_units.rst index b6cb8a96..7ce1f04a 100644 --- a/src/reference/formal_and_informative/specC_units.rst +++ b/src/reference/formal_and_informative/specC_units.rst @@ -21,4 +21,14 @@ :start-after: marker_interpretation_of_units_3 :end-before: marker_interpretation_of_units_end -.. include:: ../libcellml/libcellmlC03_interpretation_of_units.rst +.. ** THIS IS WHERE THE UNITS_REFERENCE SECTION STARTS ** + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_units_reference_start + :end-before: marker_units_reference1 + +.. include:: ../informative/informC02_units_reference.rst + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_units_reference1 + :end-before: marker_units_reference_end diff --git a/src/reference/formal_and_informative/specC_variables.rst b/src/reference/formal_and_informative/specC_variables.rst index 03d6c4d3..723f4d40 100644 --- a/src/reference/formal_and_informative/specC_variables.rst +++ b/src/reference/formal_and_informative/specC_variables.rst @@ -1,4 +1,14 @@ +.. ** PREVIOUSLY THIS WAS VARIABLE REFERENCES ** + +.. include:: ../sectionC_interpretation.inc + :start-after: marker_variable_reference_start + :end-before: marker_variable_reference_end + +.. include:: ../informative/informC05_variable_reference.rst + +.. ** PREVIOUSLY THIS WAS INTERPRETATION OF MAP_VARIABLES ** + .. include:: ../sectionC_interpretation.inc :start-after: marker_interpretation_of_map_variables_start :end-before: marker_interpretation_of_map_variables_1