prepare for MessagePack

Author: otvam

.github/SECURITY.md

@@ -4,5 +4,6 @@ To report a security issue, please email [[email protected]](mailto:guillod@otvam
 Please include a description of the issue, the steps you took to create the issue, 
 the affected versions, and, if known, mitigations for the issue. 
 
-The fact that PyPEEC is using Pickle files for storing the mesher and solver results
-is an accepted trade-off and is not considered as a security issue.
+The fact that PyPEEC can use Pickle files for storing the mesher and solver results
+is an accepted trade-off and is not considered as a security issue. Alternatively, 
+JSON/MessagePack files can be used for storing the results.

.gitignore

@@ -20,6 +20,11 @@
 *.pkl
 *.pickle
 
+# exclude msgpack files
+*.mpk
+*.msg
+*.msgpack
+
 # exclude cache directories
 **/__pycache__
 

docs/content/formats.rst

@@ -8,7 +8,7 @@ PyPEEC Workflow
 
    Description of the PyPEEC workflow (mesher, viewer, solver, and plotter).
    The input files (geometry, problem, tolerance, plotter, and viewer) are either in JSON or YAML formats.
-   The output files (voxel and solution) are either in JSON or Pickle formats.
+   The output files (voxel and solution) are either in JSON or MessagePack or Pickle formats.
 
 Geometry File Format
 --------------------

docs/content/technical.rst

@@ -57,8 +57,8 @@ For the logging, PyPEEC is using **SciLogger**:
 For the serialization, PyPEEC is using **SciSave**:
 
 * The input/configuration files are either JSON or YAML files.
-* The output/data files are either JSON or Pickle files.
-* Pickle is faster than JSON for large output/data files.
+* The output/data files are either JSON or MessagePack or Pickle files.
+* Pickle/MessagePack files are faster than JSON for large output/data files.
 * More information on the serialization module: https://github.com/otvam/scisave
 
 Packaging and Environment

docs/content/warnings.rst

@@ -59,7 +59,7 @@ General Issues
 .. warning::
     Python **Pickle files** can be used to store the mesher and solver results.
     Pickling data is not secure. Only load Pickle files that you trust.
-    JSON or GZIP/JSON files can be used to solve this problem.
+    JSON/MessagePack files can be used to solve this problem.
 
 .. warning::
     The **Docker image** is only intended for test purposes.

docs/content/workflow.rst

@@ -8,7 +8,7 @@ PyPEEC Workflow
 
    Description of the PyPEEC workflow (mesher, viewer, solver, and plotter).
    The input files (geometry, problem, tolerance, plotter, and viewer) are either in JSON or YAML formats.
-   The output files (voxel and solution) are either in JSON or Pickle formats.
+   The output files (voxel and solution) are either in JSON or MessagePack or Pickle formats.
 
 PyPEEC Tools
 ------------

pypeec/main.py

@@ -68,7 +68,7 @@ def run_mesher_file(file_geometry, file_voxel):
         - This input file is loaded by this function (JSON or YAML format).
     file_voxel : filename
         - The file content describes the meshed voxel structure.
-        - This output file is created by this function (JSON or Pickle format).
+        - This output file is created by this function (JSON or MessagePack or Pickle format).
     """
 
     # load data
@@ -150,7 +150,7 @@ def run_viewer_file(file_voxel, file_viewer, **kwargs):
     ----------
     file_voxel : filename
         - The file content describes the meshed voxel structure.
-        - This input file is loaded by this function (JSON or Pickle format).
+        - This input file is loaded by this function (JSON or MessagePack or Pickle format).
     file_viewer: filename
         - The file content describes the different plots to be created.
         - This input file is loaded by this function (JSON or YAML format).
@@ -240,7 +240,7 @@ def run_solver_file(file_voxel, file_problem, file_tolerance, file_solution):
     ----------
     file_voxel : filename
         - The file content describes the meshed voxel structure.
-        - This input file is loaded by this function (JSON or Pickle format).
+        - This input file is loaded by this function (JSON or MessagePack or Pickle format).
     file_problem: filename
         - The file content describes the problem to be solved.
         - This input file is loaded by this function (JSON or YAML format).
@@ -249,7 +249,7 @@ def run_solver_file(file_voxel, file_problem, file_tolerance, file_solution):
         - This input file is loaded by this function (JSON or YAML format).
     file_solution : filename
         - The file content describes the problem solution.
-        - This output file is created by this function (JSON or Pickle format).
+        - This output file is created by this function (JSON or MessagePack or Pickle format).
     """
 
     # load data
@@ -336,7 +336,7 @@ def run_plotter_file(file_solution, file_plotter, **kwargs):
     ----------
     file_solution : filename
         - The dict describes the problem solution.
-        - This input file is loaded by this function (JSON or Pickle format).
+        - This input file is loaded by this function (JSON or MessagePack or Pickle format).
     file_plotter : filename
         - The dict describes the different plots to be created.
         - This input file is loaded by this function (JSON or YAML format).