morphio 2.5.3__tar.gz → 2.6.1__tar.gz

{MorphIO-2.5.3 → MorphIO-2.6.1}/.github/workflows/publish-sdist-wheels.yml

@@ -12,7 +12,7 @@ env:
   # Only build on Python 3.x
   CIBW_BUILD: 'cp3?-*'
   CIBW_SKIP: 'cp35-* cp39-* *-manylinux_i686'
-  CIBW_BEFORE_TEST: pip install nose mock h5py numpy
+  CIBW_BEFORE_TEST: pip install -r {project}/tests/requirement_tests.txt
   CIBW_TEST_COMMAND: nosetests -s -v -P {project}/tests
 
 jobs:

{MorphIO-2.5.3 → MorphIO-2.6.1}/MorphIO.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.5.3
+Version: 2.6.1
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -356,7 +356,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the H5 specification
         https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
         
@@ -501,7 +501,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         A marker is an [s-expression](https://fr.wikipedia.org/wiki/S-expression) at the top level of the Neurolucida file that contains additional information about the morphology. For example:
         
         ```lisp
@@ -535,17 +535,40 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
             (9 10 11 6)
             )
             ```
-        - An sexp with one of the following top level s-exp:
-          * Dot
-          * FilledCircle
-          * SnowFlake
-          * Asterisk
-          * OpenCircle
-          * OpenStar
-          * Flower
-          * OpenSquare
-          * FilledStar
-          * DoubleCircle
+        - An sexp with one of the following top level regular expression:
+        
+          - Dot[0-9]*
+          - Plus[0-9]*
+          - Cross[0-9]*
+          - Splat[0-9]*
+          - Flower[0-9]*
+          - Circle[0-9]*
+          - Flower[0-9]*
+          - TriStar[0-9]*
+          - OpenStar[0-9]*
+          - Asterisk[0-9]*
+          - SnowFlake[0-9]*
+          - OpenCircle[0-9]*
+          - ShadedStar[0-9]*
+          - FilledStar[0-9]*
+          - TexacoStar[0-9]*
+          - MoneyGreen[0-9]*
+          - DarkYellow[0-9]*
+          - OpenSquare[0-9]*
+          - OpenDiamond[0-9]*
+          - CircleArrow[0-9]*
+          - CircleCross[0-9]*
+          - OpenQuadStar[0-9]*
+          - DoubleCircle[0-9]*
+          - FilledSquare[0-9]*
+          - MalteseCross[0-9]*
+          - FilledCircle[0-9]*
+          - FilledDiamond[0-9]*
+          - FilledQuadStar[0-9]*
+          - OpenUpTriangle[0-9]*
+          - FilledUpTriangle[0-9]*
+          - OpenDownTriangle[0-9]*
+          - FilledDownTriangle[0-9]*
         
           Example:
           ```lisp
@@ -578,6 +601,26 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         assert_array_equal(pia.diameters, [3, 4, 5, 6])
         ```
         
+        ⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
+        
+        ```python
+        ( (Color White)  ; [10,1]
+          (Dendrite)
+          ( -290.87  -113.09   -16.32     2.06)  ; Root
+          ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+          (
+            ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+            ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+            (Cross  ;  [3,3]
+              (Color Orange)
+              (Name "Marker 3")
+              ( -271.87  -121.14   -16.27     0.69)  ; 1
+              ( -269.34  -122.29   -15.48     0.69)  ; 2
+            )  ;  End of markers
+          )
+         )
+        ```
+        
         </details>
         
         ### Tips
@@ -601,11 +644,11 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         # H5v2
         
-        Starting at version 2.5.2, the file format `h5v2` is no longer supported.
-        If you have morphologies in this format, you can convert them with:
+        Starting at version 2.6.0, the file format `h5v2` is no longer supported.
+        If you have morphologies in this format, you can convert them to h5v1 with:
         
         ```bash
-        pip install morphio==2.5.1 morph-tool==2.3.0
+        pip install "morphio<2.6" "morph-tool==2.3.0"
         ```
         
         and then:

{MorphIO-2.5.3 → MorphIO-2.6.1}/MorphIO.egg-info/SOURCES.txt

@@ -171,5 +171,4 @@ tests/data/h5/v1/simple-negative-section-type.h5
 tests/data/h5/v1/simple.h5
 tests/data/h5/v1/soma_no_neurites.h5
 tests/data/h5/v1/two_child_unmerged.h5
-tests/data/h5/v2/Neuron.h5
-tests/data/h5/v2/no-metadata.h5
+tests/data/h5/v2/Neuron.h5

{MorphIO-2.5.3 → MorphIO-2.6.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: MorphIO
-Version: 2.5.3
+Version: 2.6.1
 Summary: A neuron morphology IO library
 Home-page: https://github.com/BlueBrain/MorphIO/
 Author: Blue Brain Project, EPFL
@@ -356,7 +356,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the H5 specification
         https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
         
@@ -501,7 +501,7 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         <details>
           <summary>Click to expand!</summary>
-          
+        
         A marker is an [s-expression](https://fr.wikipedia.org/wiki/S-expression) at the top level of the Neurolucida file that contains additional information about the morphology. For example:
         
         ```lisp
@@ -535,17 +535,40 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
             (9 10 11 6)
             )
             ```
-        - An sexp with one of the following top level s-exp:
-          * Dot
-          * FilledCircle
-          * SnowFlake
-          * Asterisk
-          * OpenCircle
-          * OpenStar
-          * Flower
-          * OpenSquare
-          * FilledStar
-          * DoubleCircle
+        - An sexp with one of the following top level regular expression:
+        
+          - Dot[0-9]*
+          - Plus[0-9]*
+          - Cross[0-9]*
+          - Splat[0-9]*
+          - Flower[0-9]*
+          - Circle[0-9]*
+          - Flower[0-9]*
+          - TriStar[0-9]*
+          - OpenStar[0-9]*
+          - Asterisk[0-9]*
+          - SnowFlake[0-9]*
+          - OpenCircle[0-9]*
+          - ShadedStar[0-9]*
+          - FilledStar[0-9]*
+          - TexacoStar[0-9]*
+          - MoneyGreen[0-9]*
+          - DarkYellow[0-9]*
+          - OpenSquare[0-9]*
+          - OpenDiamond[0-9]*
+          - CircleArrow[0-9]*
+          - CircleCross[0-9]*
+          - OpenQuadStar[0-9]*
+          - DoubleCircle[0-9]*
+          - FilledSquare[0-9]*
+          - MalteseCross[0-9]*
+          - FilledCircle[0-9]*
+          - FilledDiamond[0-9]*
+          - FilledQuadStar[0-9]*
+          - OpenUpTriangle[0-9]*
+          - FilledUpTriangle[0-9]*
+          - OpenDownTriangle[0-9]*
+          - FilledDownTriangle[0-9]*
         
           Example:
           ```lisp
@@ -578,6 +601,26 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         assert_array_equal(pia.diameters, [3, 4, 5, 6])
         ```
         
+        ⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
+        
+        ```python
+        ( (Color White)  ; [10,1]
+          (Dendrite)
+          ( -290.87  -113.09   -16.32     2.06)  ; Root
+          ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+          (
+            ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+            ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+            (Cross  ;  [3,3]
+              (Color Orange)
+              (Name "Marker 3")
+              ( -271.87  -121.14   -16.27     0.69)  ; 1
+              ( -269.34  -122.29   -15.48     0.69)  ; 2
+            )  ;  End of markers
+          )
+         )
+        ```
+        
         </details>
         
         ### Tips
@@ -601,11 +644,11 @@ Description: # MorphIO [![Build Status](https://travis-ci.com/BlueBrain/MorphIO.
         
         # H5v2
         
-        Starting at version 2.5.2, the file format `h5v2` is no longer supported.
-        If you have morphologies in this format, you can convert them with:
+        Starting at version 2.6.0, the file format `h5v2` is no longer supported.
+        If you have morphologies in this format, you can convert them to h5v1 with:
         
         ```bash
-        pip install morphio==2.5.1 morph-tool==2.3.0
+        pip install "morphio<2.6" "morph-tool==2.3.0"
         ```
         
         and then:

{MorphIO-2.5.3 → MorphIO-2.6.1}/README.md

@@ -349,7 +349,7 @@ Morphology("myfile.asc", options=Option.no_duplicates|Option.nrn_order)
 
 <details>
   <summary>Click to expand!</summary>
-  
+
 MorphIO also support reading and writing glia (such as astrocytes) from/to disk according to the H5 specification
 https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
 
@@ -494,7 +494,7 @@ neuron.write('/my/out/file.h5')  # Has to be written to h5
 
 <details>
   <summary>Click to expand!</summary>
-  
+
 A marker is an [s-expression](https://fr.wikipedia.org/wiki/S-expression) at the top level of the Neurolucida file that contains additional information about the morphology. For example:
 
 ```lisp
@@ -528,17 +528,40 @@ The following s-expressions are parsed:
     (9 10 11 6)
     )
     ```
-- An sexp with one of the following top level s-exp:
-  * Dot
-  * FilledCircle
-  * SnowFlake
-  * Asterisk
-  * OpenCircle
-  * OpenStar
-  * Flower
-  * OpenSquare
-  * FilledStar
-  * DoubleCircle
+- An sexp with one of the following top level regular expression:
+
+  - Dot[0-9]*
+  - Plus[0-9]*
+  - Cross[0-9]*
+  - Splat[0-9]*
+  - Flower[0-9]*
+  - Circle[0-9]*
+  - Flower[0-9]*
+  - TriStar[0-9]*
+  - OpenStar[0-9]*
+  - Asterisk[0-9]*
+  - SnowFlake[0-9]*
+  - OpenCircle[0-9]*
+  - ShadedStar[0-9]*
+  - FilledStar[0-9]*
+  - TexacoStar[0-9]*
+  - MoneyGreen[0-9]*
+  - DarkYellow[0-9]*
+  - OpenSquare[0-9]*
+  - OpenDiamond[0-9]*
+  - CircleArrow[0-9]*
+  - CircleCross[0-9]*
+  - OpenQuadStar[0-9]*
+  - DoubleCircle[0-9]*
+  - FilledSquare[0-9]*
+  - MalteseCross[0-9]*
+  - FilledCircle[0-9]*
+  - FilledDiamond[0-9]*
+  - FilledQuadStar[0-9]*
+  - OpenUpTriangle[0-9]*
+  - FilledUpTriangle[0-9]*
+  - OpenDownTriangle[0-9]*
+  - FilledDownTriangle[0-9]*
 
   Example:
   ```lisp
@@ -571,6 +594,26 @@ assert_array_equal(pia.points,
 assert_array_equal(pia.diameters, [3, 4, 5, 6])
 ```
 
+⚠️ Only top level markers are currently supported. This means the following nested marker won't be available the the MorphIO API.
+
+```python
+( (Color White)  ; [10,1]
+  (Dendrite)
+  ( -290.87  -113.09   -16.32     2.06)  ; Root
+  ( -290.87  -113.09   -16.32     2.06)  ; R, 1
+  (
+    ( -277.14  -119.13   -18.02     0.69)  ; R-1, 1
+    ( -275.54  -119.99   -16.67     0.69)  ; R-1, 2
+    (Cross  ;  [3,3]
+      (Color Orange)
+      (Name "Marker 3")
+      ( -271.87  -121.14   -16.27     0.69)  ; 1
+      ( -269.34  -122.29   -15.48     0.69)  ; 2
+    )  ;  End of markers
+  )
+ )
+```
+
 </details>
 
 ### Tips
@@ -594,11 +637,11 @@ See https://github.com/BlueBrain/MorphIO/blob/master/doc/specification.md
 
 # H5v2
 
-Starting at version 2.5.2, the file format `h5v2` is no longer supported.
-If you have morphologies in this format, you can convert them with:
+Starting at version 2.6.0, the file format `h5v2` is no longer supported.
+If you have morphologies in this format, you can convert them to h5v1 with:
 
 ```bash
-pip install morphio==2.5.1 morph-tool==2.3.0
+pip install "morphio<2.6" "morph-tool==2.3.0"
 ```
 
 and then:

{MorphIO-2.5.3 → MorphIO-2.6.1}/binds/python/bind_misc.cpp

@@ -87,6 +87,8 @@ void bind_misc(py::module& m) {
                morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_2)
         .value("MORPHOLOGY_VERSION_H5_1_1",
                morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_1_1)
+        .value("MORPHOLOGY_VERSION_H5_1_2",
+               morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_H5_1_2)
         .value("MORPHOLOGY_VERSION_SWC_1",
                morphio::enums::MorphologyVersion::MORPHOLOGY_VERSION_SWC_1)
         .value("MORPHOLOGY_VERSION_UNDEFINED",

{MorphIO-2.5.3 → MorphIO-2.6.1}/include/morphio/enums.h

@@ -42,6 +42,7 @@ enum MorphologyVersion {
     MORPHOLOGY_VERSION_H5_1_1 = 3,
     MORPHOLOGY_VERSION_ASC_1 = 4,
     MORPHOLOGY_VERSION_SWC_1 = 101,
+    MORPHOLOGY_VERSION_H5_1_2 = 5,
     MORPHOLOGY_VERSION_UNDEFINED
 };
 std::ostream& operator<<(std::ostream& os, MorphologyVersion v);

{MorphIO-2.5.3 → MorphIO-2.6.1}/include/morphio/properties.h

@@ -151,9 +151,11 @@ struct Marker {
 };
 
 struct CellLevel {
+    CellLevel()
+        : _version(MORPHOLOGY_VERSION_UNDEFINED) {}
+    MorphologyVersion _version;
     morphio::CellFamily _cellFamily;
     SomaType _somaType;
-    MorphologyVersion _version;
     std::vector<Annotation> _annotations;
     std::vector<Marker> _markers;
 

{MorphIO-2.5.3 → MorphIO-2.6.1}/src/enums.cpp

@@ -11,6 +11,8 @@ std::ostream& operator<<(std::ostream& os, const MorphologyVersion v) {
         return os << "h5v1";
     case MORPHOLOGY_VERSION_H5_1_1:
         return os << "h5v1.1";
+    case MORPHOLOGY_VERSION_H5_1_2:
+        return os << "h5v1.2";
     case MORPHOLOGY_VERSION_H5_2:
         return os << "h5v2";
     case MORPHOLOGY_VERSION_SWC_1:

{MorphIO-2.5.3 → MorphIO-2.6.1}/src/readers/lex.cpp

@@ -162,17 +162,40 @@ class NeurolucidaLexer
         rules_.push("Dendrite", +Token::DENDRITE);
         rules_.push("CellBody", +Token::CELLBODY);
 
-        rules_.push("Dot", +Token::MARKER);
-        rules_.push("FilledCircle", +Token::MARKER);
-        rules_.push("SnowFlake", +Token::MARKER);
-        rules_.push("Asterisk", +Token::MARKER);
-        rules_.push("OpenCircle", +Token::MARKER);
-        rules_.push("OpenStar", +Token::MARKER);
-        rules_.push("Flower", +Token::MARKER);
-        rules_.push("OpenSquare", +Token::MARKER);
-        rules_.push("FilledStar", +Token::MARKER);
-        rules_.push("DoubleCircle", +Token::MARKER);
-        rules_.push("Circle[0-9]+", +Token::MARKER);
+        // The code snippet used to infer the marker list is available at:
+        // https://github.com/BlueBrain/MorphIO/pull/229
+        rules_.push("Dot[0-9]*", +Token::MARKER);
+        rules_.push("Plus[0-9]*", +Token::MARKER);
+        rules_.push("Cross[0-9]*", +Token::MARKER);
+        rules_.push("Splat[0-9]*", +Token::MARKER);
+        rules_.push("Flower[0-9]*", +Token::MARKER);
+        rules_.push("Circle[0-9]*", +Token::MARKER);
+        rules_.push("Flower[0-9]*", +Token::MARKER);
+        rules_.push("TriStar[0-9]*", +Token::MARKER);
+        rules_.push("OpenStar[0-9]*", +Token::MARKER);
+        rules_.push("Asterisk[0-9]*", +Token::MARKER);
+        rules_.push("SnowFlake[0-9]*", +Token::MARKER);
+        rules_.push("OpenCircle[0-9]*", +Token::MARKER);
+        rules_.push("ShadedStar[0-9]*", +Token::MARKER);
+        rules_.push("FilledStar[0-9]*", +Token::MARKER);
+        rules_.push("TexacoStar[0-9]*", +Token::MARKER);
+        rules_.push("MoneyGreen[0-9]*", +Token::MARKER);
+        rules_.push("DarkYellow[0-9]*", +Token::MARKER);
+        rules_.push("OpenSquare[0-9]*", +Token::MARKER);
+        rules_.push("OpenDiamond[0-9]*", +Token::MARKER);
+        rules_.push("CircleArrow[0-9]*", +Token::MARKER);
+        rules_.push("CircleCross[0-9]*", +Token::MARKER);
+        rules_.push("OpenQuadStar[0-9]*", +Token::MARKER);
+        rules_.push("DoubleCircle[0-9]*", +Token::MARKER);
+        rules_.push("FilledSquare[0-9]*", +Token::MARKER);
+        rules_.push("MalteseCross[0-9]*", +Token::MARKER);
+        rules_.push("FilledCircle[0-9]*", +Token::MARKER);
+        rules_.push("FilledDiamond[0-9]*", +Token::MARKER);
+        rules_.push("FilledQuadStar[0-9]*", +Token::MARKER);
+        rules_.push("OpenUpTriangle[0-9]*", +Token::MARKER);
+        rules_.push("FilledUpTriangle[0-9]*", +Token::MARKER);
+        rules_.push("OpenDownTriangle[0-9]*", +Token::MARKER);
+        rules_.push("FilledDownTriangle[0-9]*", +Token::MARKER);
 
         rules_.push("Generated", +Token::GENERATED);
         rules_.push("High", +Token::HIGH);

{MorphIO-2.5.3 → MorphIO-2.6.1}/src/readers/morphologyASC.cpp

@@ -47,7 +47,7 @@ bool is_end_of_section(Token id) {
 bool skip_sexp(size_t id) {
     return (id == +Token::WORD || id == +Token::COLOR || id == +Token::GENERATED ||
             id == +Token::HIGH || id == +Token::INCOMPLETE || id == +Token::LOW ||
-            id == +Token::NORMAL || id == +Token::FONT);
+            id == +Token::NORMAL || id == +Token::FONT || id == +Token::MARKER);
 }
 }  // namespace