remove unused dependency(sh) (#11)

CHANGELOG.rst

@@ -1,6 +1,24 @@
 Changelog
 =========
 
+Version 4.1.2 (2024-10-17)
+--------------------------
+
+Improvements
+~~~~~~~~~~~~
+
+- Upgrade requirements.txt.
+
+
+Version 4.1.1 (2024-09-09)
+--------------------------
+
+Improvements
+~~~~~~~~~~~~
+
+- Upgrade requirements.txt.
+
+
 Version 4.1.0 (2024-08-28)
 --------------------------
 

bbp_workflow/settings.py

@@ -28,7 +28,7 @@
 
 HTTPS_PROXY = "http://bbpproxy.epfl.ch:80/"
 
-MODULE_ARCHIVE = "archive/2024-06"
+MODULE_ARCHIVE = "archive/2024-09"
 
 CFG_JSON = "config.json"
 SIM_CFG_JSON = "simulation_config.json"

pyproject.toml

@@ -29,7 +29,6 @@ dependencies = [
   "luigi",
   "jsonschema",
   "luigi-tools",
-  "sh<2",
   "matplotlib",
   "bluepysnap",
   "voxcell",

requirements.txt

@@ -1,12 +1,12 @@
 #
-# This file is autogenerated by pip-compile with Python 3.11
+# This file is autogenerated by pip-compile with Python 3.12
 # by the following command:
 #
 #    pip-compile
 #
 annotated-types==0.7.0
     # via pydantic
-anyio==4.4.0
+anyio==4.6.2.post1
     # via httpx
 appdirs==1.4.4
     # via pint
@@ -21,19 +21,19 @@ attrs==24.2.0
     #   referencing
 blue-cwl==1.0.0
     # via bbp-workflow (setup.py)
-bluepyefe==2.3.34
+bluepyefe==2.3.35
     # via bluepyemodel
-bluepyemodel==1.0.17
+bluepyemodel==1.0.24
     # via bbp-workflow (setup.py)
-bluepyopt==1.14.15
+bluepyopt==1.14.16
     # via bluepyemodel
 bluepysnap==3.0.1
     # via
     #   bbp-workflow (setup.py)
     #   brainbuilder
 brainbuilder==0.20.1
     # via blue-cwl
-brayns==3.9.0
+brayns==3.10.0
     # via bbp-workflow (setup.py)
 cached-property==1.5.2
     # via
@@ -46,7 +46,7 @@ certifi==2024.8.30
     #   requests
 cffi==1.17.1
     # via cryptography
-charset-normalizer==3.3.2
+charset-normalizer==3.4.0
     # via requests
 cheetah3==3.2.6.post1
     # via bbp-workflow (setup.py)
@@ -67,13 +67,13 @@ contourpy==1.3.0
     # via matplotlib
 cryptography==43.0.1
     # via jwcrypto
-currentscape==1.0.15
+currentscape==1.0.16
     # via bluepyemodel
 cycler==0.12.1
     # via matplotlib
 deap==1.4.1
     # via bluepyopt
-debugpy==1.8.5
+debugpy==1.8.7
     # via ipykernel
 decorator==5.1.1
     # via
@@ -85,14 +85,14 @@ deprecation==2.1.0
     #   python-keycloak
 docutils==0.21.2
     # via python-daemon
-efel==5.7.9
+efel==5.7.10
     # via
     #   bluepyefe
     #   bluepyemodel
     #   bluepyopt
 elephant==1.1.0
     # via bbp-workflow (setup.py)
-entity-management==1.5.2
+entity-management==1.6.0
     # via
     #   bbp-workflow (setup.py)
     #   blue-cwl
@@ -108,51 +108,51 @@ flexcache==0.3
     # via pint
 flexparser==0.3.1
     # via pint
-fonttools==4.53.1
+fonttools==4.54.1
     # via matplotlib
-fz-td-recipe==0.2.3
+fz-td-recipe==0.2.4
     # via blue-cwl
 gitdb==4.0.11
     # via gitpython
 gitpython==3.1.43
     # via bluepyemodel
 h11==0.14.0
     # via httpcore
-h5py==3.11.0
+h5py==3.12.1
     # via
     #   bluepyefe
     #   bluepysnap
     #   brainbuilder
     #   hdmf
     #   pynwb
     #   voxcell
-hdmf==3.14.4
+hdmf==3.14.5
     # via pynwb
-httpcore==1.0.5
+html5lib-modern==1.2
+    # via rdflib
+httpcore==1.0.6
     # via httpx
 httpx==0.27.2
     # via python-keycloak
-idna==3.8
+idna==3.10
     # via
     #   anyio
     #   httpx
     #   requests
 igor2==0.5.8
     # via bluepyefe
-importlib-resources==6.4.4
+importlib-resources==6.4.5
     # via bluepysnap
 ipykernel==6.29.5
     # via ipyparallel
 ipyparallel==8.8.0
     # via
     #   bluepyemodel
     #   bluepyopt
-ipython==8.27.0
+ipython==8.28.0
     # via
     #   ipykernel
     #   ipyparallel
-isodate==0.6.1
-    # via rdflib
 jedi==0.19.1
     # via ipython
 jinja2==3.1.4
@@ -172,9 +172,9 @@ jsonschema==4.23.0
     #   fz-td-recipe
     #   hdmf
     #   luigi-tools
-jsonschema-specifications==2023.12.1
+jsonschema-specifications==2024.10.1
     # via jsonschema
-jupyter-client==8.6.2
+jupyter-client==8.6.3
     # via
     #   ipykernel
     #   ipyparallel
@@ -206,7 +206,7 @@ lxml==5.3.0
     # via
     #   brainbuilder
     #   fz-td-recipe
-markupsafe==2.1.5
+markupsafe==3.0.1
     # via jinja2
 matplotlib==3.9.2
     # via
@@ -222,12 +222,12 @@ more-itertools==10.5.0
     # via
     #   bluepysnap
     #   morph-tool
-morph-tool==2.11.0
+morph-tool==2.11.2
     # via
     #   blue-cwl
     #   bluepyemodel
     #   bluepysnap
-morphio==3.3.9
+morphio==3.4.0
     # via
     #   bluepyemodel
     #   bluepysnap
@@ -242,7 +242,7 @@ neo==0.13.3
     #   elephant
 nest-asyncio==1.6.0
     # via ipykernel
-neurom==4.0.2
+neurom==4.0.4
     # via
     #   bluepyemodel
     #   morph-tool
@@ -296,7 +296,7 @@ packaging==24.1
     #   xarray
 palettable==3.3.3
     # via currentscape
-pandas[pyarrow]==2.2.2
+pandas[pyarrow]==2.2.3
     # via
     #   bbp-workflow (setup.py)
     #   blue-cwl
@@ -319,15 +319,15 @@ pexpect==4.9.0
     # via ipython
 pickleshare==0.7.5
     # via bluepyopt
-pillow==10.4.0
+pillow==11.0.0
     # via matplotlib
 pint==0.24.3
     # via pint-xarray
 pint-xarray==0.4
     # via bbp-workflow (setup.py)
-platformdirs==4.3.2
+platformdirs==4.3.6
     # via jupyter-core
-prompt-toolkit==3.0.47
+prompt-toolkit==3.0.48
     # via ipython
 psutil==6.0.0
     # via
@@ -344,19 +344,19 @@ pyarrow==17.0.0
     #   pandas
 pycparser==2.22
     # via cffi
-pydantic==2.9.1
+pydantic==2.9.2
     # via blue-cwl
-pydantic-core==2.23.3
+pydantic-core==2.23.4
     # via pydantic
 pygments==2.18.0
     # via ipython
 pyjwt==2.9.0
     # via entity-management
 pynrrd==1.0.0
     # via voxcell
-pynwb==2.8.1
+pynwb==2.8.2
     # via efel
-pyparsing==3.1.4
+pyparsing==3.2.0
     # via
     #   matplotlib
     #   rdflib
@@ -371,9 +371,9 @@ python-dateutil==2.9.0.post0
     #   matplotlib
     #   pandas
     #   pynwb
-python-keycloak==4.3.0
+python-keycloak==4.6.2
     # via entity-management
-pytz==2024.1
+pytz==2024.2
     # via pandas
 pyyaml==6.0.2
     # via
@@ -390,7 +390,7 @@ quantities==0.15.0
     # via
     #   elephant
     #   neo
-rdflib==7.0.0
+rdflib==7.1.0
     # via
     #   entity-management
     #   sparqlwrapper
@@ -425,13 +425,10 @@ scipy==1.14.1
     #   morph-tool
     #   neurom
     #   voxcell
-sh==1.14.3
-    # via bbp-workflow (setup.py)
 six==1.16.0
     # via
     #   asttokens
     #   elephant
-    #   isodate
     #   python-dateutil
 smmap==5.0.1
     # via gitdb
@@ -472,16 +469,15 @@ typing-extensions==4.12.2
     #   efel
     #   flexcache
     #   flexparser
-    #   ipython
     #   jwcrypto
     #   luigi-tools
     #   pint
     #   pydantic
     #   pydantic-core
     #   pynrrd
-tzdata==2024.1
+tzdata==2024.2
     # via pandas
-urllib3==2.2.2
+urllib3==2.2.3
     # via requests
 voxcell==3.1.9
     # via
@@ -490,13 +486,13 @@ voxcell==3.1.9
     #   brainbuilder
 wcwidth==0.2.13
     # via prompt-toolkit
-websockets==13.0.1
+websockets==13.1
     # via brayns
-xarray==2024.7.0
+xarray==2024.9.0
     # via
     #   bbp-workflow (setup.py)
     #   pint-xarray
-xmltodict==0.13.0
+xmltodict==0.14.2
     # via morph-tool
 
 # The following packages are considered to be unsafe in a requirements file: