Reboot with new cookiecutter version, lots of fixes and fix commit history

Co-authored-by: JavierGOrdonnez  <[email protected]>

Author: lmoyasans

Makefile

@@ -1,5 +1,5 @@
 #
-# Author: Lucia Moya-Sans
+# Author: Lucia Moya Sans
 
 SHELL = /bin/sh
 .DEFAULT_GOAL := help
@@ -9,117 +9,59 @@ export VCS_REF    := $(shell git rev-parse --short HEAD 2> /dev/null || echo unv
 export VCS_STATUS := $(if $(shell git status -s 2> /dev/null || echo unversioned repo),'modified/untracked','clean')
 export BUILD_DATE := $(shell date -u +"%Y-%m-%dT%H:%M:%SZ")
 
-export DOCKER_REGISTRY   ?= itisfoundation
 export DOCKER_IMAGE_NAME ?= pymorphosonic
-export DOCKER_IMAGE_TAG  ?= $(shell cat VERSION 2> /dev/null || echo undefined)
-
+export DOCKER_IMAGE_TAG ?= 0.1.0
 
 OSPARC_DIR:=$(CURDIR)/.osparc
 
 APP_NAME := pymorphosonic
 
+# Builds new service version ----------------------------------------------------------------------------
 
-
-
-# INTEGRATION -----------------------------------------------------------------
-METADATA := .osparc/metadata.yml
-
-
-.PHONY: VERSION
-VERSION: $(METADATA) ## generates VERSION from metadata
-	# updating $@ from $<
-	@$(OSPARC_DIR)/bin/ooil get-version --metadata-file $< > $@
-
-service.cli/run: $(METADATA) ## generates run from metadata
-	# Updates adapter script from metadata in $<
-	@$(OSPARC_DIR)/bin/ooil run-creator --metadata $< --runscript $@
-
-docker-compose.yml: $(METADATA) ## generates docker-compose
-	# Injects metadata from $< as labels
-	@$(OSPARC_DIR)/bin/ooil compose --to-spec-file $@ --metadata $<
-
-
-
-# BUILD -----------------------------------------------------------------
-
-define _docker_compose_build
-export DOCKER_BUILD_TARGET=$(if $(findstring -devel,$@),development,$(if $(findstring -cache,$@),cache,production)); \
-	docker compose -f docker-compose.yml build $(if $(findstring -nc,$@),--no-cache,);
-endef
-
-
-.PHONY: build build-devel build-nc build-devel-nc
-build build-devel build-nc build-devel-nc: VERSION docker-compose.yml service.cli/run ## builds image
-	# building image local/${DOCKER_IMAGE_NAME}...
-	@$(call _docker_compose_build)
-
-define show-meta
-	$(foreach iid,$(shell docker images */$(1):* -q | sort | uniq),\
-		docker image inspect $(iid) | jq '.[0] | .RepoTags, .ContainerConfig.Labels, .Config.Labels';)
+define _bumpversion
+	# upgrades as $(subst $(1),,$@) version, commits and tags
+	@docker run -it --rm -v $(PWD):/${DOCKER_IMAGE_NAME} \
+		-u $(shell id -u):$(shell id -g) \
+		itisfoundation/ci-service-integration-library:latest \
+		sh -c "cd /${DOCKER_IMAGE_NAME} && bump2version --verbose --list --config-file $(1) $(subst $(2),,$@)"
 endef
 
+.PHONY: version-patch version-minor version-major
+version-patch version-minor version-major: .bumpversion.cfg ## increases service's version
+	@make compose-spec
+	@$(call _bumpversion,$<,version-)
+	@make compose-spec
 
-.PHONY: info-build
-info-build: ## displays info on the built image
-	# Built images
-	@docker images */$(DOCKER_IMAGE_NAME):*
-	# Tags and labels
-	@$(call show-meta,$(DOCKER_IMAGE_NAME))
-
-
-# TESTS-----------------------------------------------------------------
-.PHONY: test tests
-test tests:  ## runs validation tests
-	@$(OSPARC_DIR)/bin/ooil test .
-
-
-
-# PUBLISHING -----------------------------------------------------------------
+.PHONY: compose-spec
+compose-spec: ## runs ooil to assemble the docker-compose.yml file
+	@docker run --rm -v $(PWD):/${DOCKER_IMAGE_NAME} \
+		-u $(shell id -u):$(shell id -g) \
+		itisfoundation/ci-service-integration-library:latest \
+		sh -c "cd /${DOCKER_IMAGE_NAME} && ooil compose"
 
-.PHONY: version-service-patch version-service-minor version-service-major
-version-service-patch version-service-minor version-service-major: $(METADATA) ## kernel/service versioning as patch
-	$(OSPARC_DIR)/bin/ooil bump-version --metadata-file $<  --upgrade $(subst version-service-,,$@)
-	# syncing metadata upstream
-	@$(MAKE) VERSION
+build: | compose-spec	## build docker image
+	docker compose build
 
-
-.PHONY: tag-local
-tag-local:
-	docker tag ${DOCKER_REGISTRY}/${DOCKER_IMAGE_NAME}:$(if $(findstring version,$@),$(DOCKER_IMAGE_NAME),latest) local/$(DOCKER_IMAGE_NAME):production
-
-.PHONY: push push-force push-version push-latest pull-latest pull-version tag-latest tag-version
-tag-latest tag-version:
-	docker tag simcore/services/comp/${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG} $(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(if $(findstring version,$@),$(DOCKER_IMAGE_TAG),latest)
-
-version_valid  = $(shell test $$(echo $(DOCKER_IMAGE_TAG) | cut --fields=1 --delimiter=.) -gt 0 > /dev/null && echo "image version is valid")
-version_exists = $(shell DOCKER_CLI_EXPERIMENTAL=enabled docker manifest inspect $(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG) > /dev/null && echo "image already exists on $(DOCKER_REGISTRY)")
-push push-force: ## pushes (resp. force) services to the registry if service not available in registry.
-	@$(if $(findstring force,$@),,\
-		$(if $(call version_valid),$(info version is valid), $(error $(DOCKER_IMAGE_TAG) is not a valid version (major>=1)))\
-		$(if $(call version_exists),$(error $(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG) already exists on $(DOCKER_REGISTRY)), $(info no version found on $(DOCKER_REGISTRY)))\
-	)
-	@$(MAKE) push-version;
-	@$(MAKE) push-latest;
+# To test built service locally -------------------------------------------------------------------------
+.PHONY: run-local
+run-local:	## runs image with local configuration
+	docker compose --file docker-compose-local.yml up
 
 .PHONY: publish-local
 publish-local: ## push to local throw away registry to test integration
 	docker tag simcore/services/comp/${DOCKER_IMAGE_NAME}:${DOCKER_IMAGE_TAG} registry:5000/simcore/services/comp/$(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG)
 	docker push registry:5000/simcore/services/comp/$(DOCKER_IMAGE_NAME):$(DOCKER_IMAGE_TAG)
 	@curl registry:5000/v2/_catalog | jq
-	
-push-latest push-version: ## publish service to registry with latest/version tag
-	# pushing '$(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(if $(findstring version,$@),$(DOCKER_IMAGE_TAG),latest)'...
-	@$(MAKE) tag-$(subst push-,,$@)
-	@docker push $(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(if $(findstring version,$@),$(DOCKER_IMAGE_TAG),latest)
-	# pushed '$(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(if $(findstring version,$@),$(DOCKER_IMAGE_TAG),latest)'
-
-pull-latest pull-version: ## pull service from registry
-	@docker pull $(DOCKER_REGISTRY)/$(DOCKER_IMAGE_NAME):$(if $(findstring version,$@),$(DOCKER_IMAGE_TAG),latest)
-
 
+.PHONY: help
+help: ## this colorful help
+	@echo "Recipes for '$(notdir $(CURDIR))':"
+	@echo ""
+	@awk 'BEGIN {FS = ":.*?## "} /^[[:alpha:][:space:]_-]+:.*?## / {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
+	@echo ""
 
 
-# COOCKIECUTTER -----------------------------------------------------------------
+# COOKIECUTTER -----------------------------------------------------------------
 
 .PHONY: replay
 replay: .cookiecutterrc ## re-applies cookiecutter
@@ -130,16 +72,13 @@ replay: .cookiecutterrc ## re-applies cookiecutter
 		"gh:ITISFoundation/cookiecutter-osparc-service"
 
 
-
 .PHONY: info
 info: ## general info
 	# env vars: version control
 	@echo " VCS_URL                     : $(VCS_URL)"
 	@echo " VCS_REF                     : $(VCS_REF)"
 	@echo " VCS_STATUS                  : $(VCS_STATUS)"
 	# env vars: docker
-	@echo " DOCKER_REGISTRY             : $(DOCKER_REGISTRY)"
-	@echo " DOCKER_IMAGE_NAME           : $(DOCKER_IMAGE_NAME)"
 	@echo " DOCKER_IMAGE_TAG            : $(DOCKER_IMAGE_TAG)"
 	@echo " BUILD_DATE                  : $(BUILD_DATE)"
 	# exe: recommended dev tools
@@ -150,21 +89,10 @@ info: ## general info
 	@echo ' python                      : $(shell python3 --version 2>/dev/null || echo not found )'
 	@echo ' docker                      : $(shell docker --version)'
 	@echo ' docker buildx               : $(shell docker buildx version)'
-	@echo ' docker-compose              : $(shell docker-compose --version)'
-	# exe: integration tools
-	@echo ' ooil version                : $(shell $(OSPARC_DIR)/bin/ooil --version)'
-
-
+	@echo ' docker compose              : $(shell docker compose --version)'
 
 # MISC -----------------------------------------------------------------
 
-.PHONY: help
-help: ## this colorful help
-	@echo "Recipes for '$(notdir $(CURDIR))':"
-	@echo ""
-	@awk --posix 'BEGIN {FS = ":.*?## "} /^[[:alpha:][:space:]_-]+:.*?## / {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}' $(MAKEFILE_LIST)
-	@echo ""
-
 
 .PHONY: clean
 git_clean_args = -dxf --exclude=.vscode/
@@ -174,4 +102,4 @@ clean: ## cleans all unversioned files in project and temp files create by this
 	@git clean -n $(git_clean_args)
 	@echo -n "Are you sure? [y/N] " && read ans && [ $${ans:-N} = y ]
 	@echo -n "$(shell whoami), are you REALLY sure? [y/N] " && read ans && [ $${ans:-N} = y ]
-	@git clean $(git_clean_args)
+	@git clean $(git_clean_args)

docker-compose-local.yml

@@ -0,0 +1,7 @@
+version: '3.7'
+services:
+  pymorphosonic:
+    image: simcore/services/comp/pymorphosonic:0.1.0
+    volumes:
+      - ${PWD}/validation/input:/tmp/input
+      - ${PWD}/validation/output:/tmp/output

docker-compose.yml

@@ -1,29 +1,31 @@
+version: '3.7'
 services:
   pymorphosonic:
     build:
       context: ./
       dockerfile: docker/python/Dockerfile
       labels:
-        io.simcore.name: '{"name":"PyMorphosonic"}'
+        io.simcore.name: '{"name":"pymorphosonic"}'
         io.simcore.thumbnail: '{"thumbnail":"https://github.com/ITISFoundation/osparc-assets/blob/cb43207b6be2f4311c93cd963538d5718b41a023/assets/default-thumbnail-cookiecutter-osparc-service.png?raw=true"}'
-        io.simcore.description: '{"description":"Computational service for simulations
-          with Pysonic and Morphosonic"}'
+        io.simcore.description: '{"description":"pymorphosonic"}'
         io.simcore.key: '{"key":"simcore/services/comp/pymorphosonic"}'
         io.simcore.version: '{"version":"0.1.0"}'
         io.simcore.integration-version: '{"integration-version":"1.0.0"}'
         io.simcore.type: '{"type":"computational"}'
-        io.simcore.authors: '{"authors":[{"name":"Lucia Moya-Sans","email":"moyasans@itis.swiss","affiliation":"ITIS
-          Research Foundation"}]}'
+        io.simcore.authors: '{"authors":[{"name":"Lucia Moya Sans","email":"moyasans@itis.swiss","affiliation":"ITIS
+          Foundation"}]}'
         io.simcore.contact: '{"contact":"moyasans@itis.swiss"}'
-        io.simcore.inputs: '{"inputs":{"input_1":{"displayOrder":1.0,"label":"input_data","description":"Input
-          data","type":"data:*/*","fileToKeyMap":{"input.zip":"input_1"}}}}'
-        io.simcore.outputs: '{"outputs":{"output_1":{"displayOrder":1.0,"label":"output_file","description":"The
-          output 1 description","type":"data:*/*","fileToKeyMap":{"output.zip":"output_1"}}}}'
-        org.label-schema.build-date: 2025-03-03T20:33:42+0000
+        io.simcore.inputs: '{"inputs":{"input_1":{"displayOrder":1.0,"label":"input_1_label","description":"Input
+          files (including a .py file)","type":"data:*/*"}}}'
+        io.simcore.outputs: '{"outputs":{"output_1":{"displayOrder":1.0,"label":"output_1_label","description":"The
+          input 1 description","type":"data:*/*"}}}'
+        org.label-schema.build-date: 2025-03-07T15:38:21+0000
         org.label-schema.schema-version: '1.0'
-        org.label-schema.vcs-ref: ''
-        org.label-schema.vcs-url: ''
+        org.label-schema.vcs-ref: 416e2c5b2f336cb7731ed920b2ca83f72c13d4a1
+        org.label-schema.vcs-url: https://github.com/ITISFoundation/pymorphosonic.git
         simcore.service.restart-policy: no-restart
-        simcore.service.settings: '[{"name":"Resources","type":"Resources","value":{"Limits":{"NanoCPUs":1000000000,"MemoryBytes":2147483648}}}]'
+        simcore.service.paths-mapping: '{"inputs_path":"/home/scu/work/inputs","outputs_path":"/home/scu/work/outputs"}'
+        simcore.service.settings: '[{"name":"constraints","type":"string","value":["node.platform.os
+          == linux"]},{"name":"Resources","type":"Resources","value":{"Limits":{"NanoCPUs":1000000000,"MemoryBytes":2147483648}}}]'
       target: production
     image: simcore/services/comp/pymorphosonic:0.1.0

docker/python/Dockerfile

@@ -1,14 +1,14 @@
-FROM python:3.11 AS base
+FROM python:3.11 as base
 #
 #  USAGE:
 #     cd services/pymorphosonic
 #     docker build -f Dockerfile -t pymorphosonic:prod --target production ../../
 #     docker run pymorphosonic:prod
 #
 
-LABEL maintainer=moyasans
+LABEL maintainer=lmoyasans
 
-# simcore-user uid=8004(${SC_USER_NAME}) gid=8004(${SC_USER_NAME}) groups=8004(${SC_USER_NAME}) TODO change to scu
+# simcore-user uid=8004(${SC_USER_NAME}) gid=8004(${SC_USER_NAME}) groups=8004(${SC_USER_NAME})
 ENV SC_USER_ID 8004
 ENV SC_USER_NAME scu
 RUN adduser --uid ${SC_USER_ID} --disabled-password --gecos "" --shell /bin/sh --home /home/${SC_USER_NAME} ${SC_USER_NAME}
@@ -18,98 +18,29 @@ RUN apt-get update \
     jq \
     && rm --recursive --force /var/lib/apt/lists/*
 
-# -------------------------- Build stage -------------------
-# Installs build/package management tools and third party dependencies
-#
-# + /build             WORKDIR
-#
-
-FROM base AS build
-
-ENV SC_BUILD_TARGET build
-
-# ------------------------------------------------------------------------------------
-#TODO:
-# uncomment and adapt if build dependencies shall be installed
-#RUN apt-get update \
-# && apt-get -y install --no-install-recommends \
-# gcc \
-# git \
-# && rm -rf /var/lib/apt/lists/*
-
-# uncomment and adapt if python necessary
-#RUN $SC_PIP install --upgrade pip wheel setuptools
-# ------------------------------------------------------------------------------------
-
-WORKDIR /build
-# defines the output of the build
-RUN mkdir --parents /build/bin
-# copy src code
-COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} src/pymorphosonic src/pymorphosonic
-
-# ------------------------------------------------------------------------------------
-#TODO:
-# uncomment and adapt if build steps are necessary
-# RUN cp -R src/pymorphosonic/* /build/bin
-# ------------------------------------------------------------------------------------
-
-# --------------------------Production stage -------------------
-# Final cleanup up to reduce image size and startup setup
-# Runs as ${SC_USER_NAME} (non-root user)
-#
-#  + /home/${SC_USER_NAME}     $HOME = WORKDIR
-#    + pymorphosonic [${SC_USER_NAME}:${SC_USER_NAME}]
-#    + docker [${SC_USER_NAME}:${SC_USER_NAME}]
-#    + service.cli [${SC_USER_NAME}:${SC_USER_NAME}]
-#
-FROM base AS production
+FROM base as production
 
 ENV SC_BUILD_TARGET production
 ENV SC_BOOT_MODE production
 
-
-ENV INPUT_FOLDER="/input" \
-    OUTPUT_FOLDER="/output"
-
+ENV INPUT_FOLDER="/tmp/input" \
+    OUTPUT_FOLDER="/tmp/output"
 
 WORKDIR /home/${SC_USER_NAME}
 
-# ------------------------------------------------------------------------------------
-#TODO:
-# uncomment and adapt to install runtime dependencies
-#RUN apt-get update \
-# && apt-get -y install --no-install-recommends \
-# && rm -rf /var/lib/apt/lists/*
-# ------------------------------------------------------------------------------------
+RUN pip install -e git+https://github.com/tjjlemaire/PySONIC.git@aff881012b83731e7139aa1994f5dff358525700#egg=pysonic
+RUN pip install -e git+https://github.com/tjjlemaire/MorphoSONIC.git@64a0a2325ec8a1cfa90ce5595ea93301e4a1ff91#egg=morphosonic
 
 # copy docker bootup scripts
 COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} docker/python/*.sh docker/
+# copy src code
+COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} src/pymorphosonic src/pymorphosonic
 # copy simcore service cli
 COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} service.cli/ service.cli/
 # necessary to be able to call run directly without sh in front
 ENV PATH="/home/${SC_USER_NAME}/service.cli:${PATH}"
-
-# copy binaries from build
-COPY --from=build --chown=${SC_USER_NAME}:${SC_USER_NAME} /build/bin pymorphosonic
-COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} requirements.txt /app/
-COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} PySONIC-1.0.0-py3-none-any.whl /app/
-COPY --chown=${SC_USER_NAME}:${SC_USER_NAME} MorphoSONIC-1.0.0-py3-none-any.whl /app/
-# HOW TO COPY WHL FILE and txt 
-
-
-RUN pip install --upgrade pip wheel setuptools tqdm lockfile multiprocess boltons openpyxl
-RUN pip install -r /app/requirements.txt
-RUN pip install /app/PySONIC-1.0.0-py3-none-any.whl
-RUN pip install /app/MorphoSONIC-1.0.0-py3-none-any.whl
-# ------------------------------------------------------------------------------------
-#TODO:
-# uncomment and provide a healtchecker if possible
-# HEALTHCHECK --interval=30s \
-#             --timeout=120s \
-#             --start-period=30s \
-#             --retries=3 \
-#             CMD ["healthchecker app"]
-# ------------------------------------------------------------------------------------
+RUN pip install -r src/pymorphosonic/requirements.txt
 
 ENTRYPOINT [ "/bin/sh", "docker/entrypoint.sh", "/bin/sh", "-c" ]
-CMD ["run"]
+## only for computational (also the "/bin/sh", "-c" above)
+CMD ["run"] 

service.cli/execute.sh

@@ -1,35 +1,20 @@
-#!/bin/bash
+#!/bin/sh
 # set sh strict mode
 set -o errexit
 set -o nounset
 IFS=$(printf '\n\t')
-INFO="INFO: [$(basename "$0")] "
 
-cd /home/scu/pymorphosonic
+cd /home/scu/src/pymorphosonic
 
-echo "$INFO" "starting service as"
-echo "$INFO" "  User    :$(id "$(whoami)")"
-echo "$INFO" "  Workdir : $(pwd)"
+echo "starting service as"
+echo   User    : "$(id "$(whoami)")"
+echo   Workdir : "$(pwd)"
+echo "..."
+echo
 
-# Checking for resources limit env vars injected by osparc
-SIMCORE_NANO_CPUS_LIMIT="${SIMCORE_NANO_CPUS_LIMIT:-0}"
-if [ "${SIMCORE_NANO_CPUS_LIMIT}" -ne "0" ]
-then
-    echo "$INFO" "Found NANO_CPU limits: ${SIMCORE_NANO_CPUS_LIMIT}"
-    NANO_CPU_DIVISOR=1000000000
-    MAX_CPUS=$(("${SIMCORE_NANO_CPUS_LIMIT}" / "${NANO_CPU_DIVISOR}"))
-    # use 1 if this is 0 otherwise floor is probably fine
-    if [ "${MAX_CPUS}" -eq "0" ]
-    then
-        MAX_CPUS=1
-    fi
-    echo "$INFO" "Setting Z43_MAX_CPU_RESOURCES to " "${MAX_CPUS}"
-    export Z43_MAX_CPU_RESOURCES="${MAX_CPUS}"
-    export OMP_NUM_THREADS="${MAX_CPUS}"
-fi
+# ----------------------------------------------------------------
 
 env
-
 python3 main.py setup
 /bin/sh main.sh
-python3 main.py teardown
+python3 main.py teardown

src/pymorphosonic/main.py

@@ -8,16 +8,13 @@
 from pathlib import Path
 
 logging.basicConfig(level=logging.INFO)
-logger = logging.getLogger("s4l-python-main")
-
+logger = logging.getLogger("pymorphosonic")
 
 ENVIRONS = ["INPUT_FOLDER", "OUTPUT_FOLDER"]
 try:
     input_dir, output_dir = [Path(os.environ.get(v, None)) for v in ENVIRONS]
 except KeyError:
     raise ValueError("Required env vars {ENVIRONS} were not set")
-
-# TODO: sync with schema in metadata!!
 OUTPUT_FILE = "output_data.zip"
 
 
@@ -90,12 +87,7 @@ def ensure_requirements(code_dir: Path) -> Path:
         # deduce requirements using pipreqs
         logger.info("Not found. Recreating requirements ...")
         requirements = code_dir / "requirements.txt"
-        # TODO: MaG This currently does not work for XCore and friends
-        # run_cmd(f"pipreqs --savepath={requirements} --force {code_dir}")
         run_cmd(f"touch {requirements}")
-
-        # TODO log subprocess.run
-
     else:
         requirements = requirements[0]
     return requirements
@@ -110,7 +102,7 @@ def setup():
     # NOTE The inputs defined in ${INPUT_FOLDER}/inputs.json are available as env variables by their key in capital letters
     # For example: input_1 -> $INPUT_1
     #
-
+    
     logger.info("Processing input ...")
     unzip_dir(input_dir)
 
@@ -125,13 +117,15 @@ def setup():
     requirements_txt = ensure_requirements(input_dir)
 
     logger.info("Preparing launch script ...")
-    venv_dir = Path(os.getenv("SC_PYTHON_VENV_ROOT_DIR"))
+    venv_dir = Path.home() / ".venv"
     # TODO: pipreqs tries to download XCore. Can that be avoided?
     script = [
         "#!/bin/sh",
         "set -o errexit",
         "set -o nounset",
         "IFS=$(printf '\\n\\t')",
+        'echo "Creating virtual environment ..."',
+        f'python3 -m venv --system-site-packages --symlinks --upgrade "{venv_dir}"',
         f'echo Installing requirements from "{requirements_txt}"',
         f"echo Currently installed packages:",
         f'"{venv_dir}"/bin/pip list',
@@ -181,4 +175,4 @@ def teardown():
         else:
             teardown()
     except Exception as err:  # pylint: disable=broad-except
-        logger.error("%s . Stopping %s", err, action)
+        logger.error("%s . Stopping %s", err, action)

src/pymorphosonic/requirements.txt

@@ -0,0 +1,9 @@
+tqdm>=4.3
+lockfile>=0.1.2
+multiprocess>=0.70
+boltons>=20.1.0
+openpyxl
+jupyterlab
+#  matplotlib requirements
+contourpy==1.3.0
+matplotlib==3.7.3

validation/input/input.json

@@ -0,0 +1,60 @@
+import pickle
+
+from PySONIC.core import PulsedProtocol, BalancedPulsedProtocol
+from PySONIC.utils import logger
+
+from MorphoSONIC.models import SennFiber
+from MorphoSONIC.sources import *
+from MorphoSONIC.plt import *
+
+
+# class GammaAcousticSource(GammaSource, AbstractAcousticSource):
+
+#     def __init__(self, gamma_dict, f, A=None):
+#         GammaSource.__init__(self, gamma_dict, f=f)
+#         AbstractAcousticSource.__init__(self, f, A=A)
+
+#     def computeDistributedAmps(self, fiber):
+#         return {k: self.A*v for k,v in GammaSource.computeDistributedAmps(self,fiber).items()}
+
+#     def copy(self):
+#         return self.__class__(self.gamma_dict, self.f, A=self.A)
+
+#     @staticmethod
+#     def inputs():
+#         return {**GammaSource.inputs(), **AbstractAcousticSource.inputs()}
+
+# a = 3.2e-08
+# fs = 1.0
+# input_path = "/home/scu/work/inputs/input_1"
+
+# with open(input_path+'/axon_details','rb') as f:
+#     axondetails = pickle.load(f)
+# with open(input_path+'/gamma_dicts','rb') as f:
+#     gamma_dicts = pickle.load(f)
+
+# fiberD = [ad[2] for ad in axondetails]
+# nnodes = [len(ad[3]) for ad in axondetails]
+
+# # Create fiber models
+# fibers = [SennFiber(fiberD, nnodes=nnodes, a=a, fs=fs) for fiberD, nnodes in zip(fiberD, nnodes)] 
+
+# tpulse = 0.0001
+# toffset = 0.0005
+# pp = PulsedProtocol(tpulse, toffset)  
+
+# gamma_source = [GammaAcousticSource(gamma_dict, f=500000.0, A=100000.0) for gamma_dict in gamma_dicts]  
+
+# data_meta_list = []
+# for fiber, source in zip(fibers, gamma_source): # TODO can be setted to a number
+# # Simulate model with each source-protocol pair, and plot results
+#     data, meta = fiber.simulate(source, pp)
+#     #SectionCompTimeSeries([(data, meta)], 'Vm', fiber.nodeIDs).render()
+#     data_meta_list.append((data, meta))
+
+# output_path = "/home/jovyan/work/outputs/output_1"
+# with open(output_path+'/neuron_sims.pickle','wb') as f:
+#     pickle.dump(data_meta_list,f)
+
+print("Hello World")
+

validation/input/main.py

@@ -0,0 +1,9 @@
+tqdm>=4.3
+lockfile>=0.1.2
+multiprocess>=0.70
+boltons>=20.1.0
+openpyxl
+jupyterlab
+#  matplotlib requirements
+contourpy==1.3.0
+matplotlib==3.7.3