.codecov.yml

+fixes:
+  - "/builds/hip/datahipy/datahipy::datahipy/"

.coveragerc

@@ -3,7 +3,7 @@
 branch = False
 concurrency = multiprocessing
 parallel = True
-source = bids_tools
+source = datahipy
 # Omit files that are generated by versioneer
 omit = */_version.py
 

.gitattributes

-bids_tools/_version.py export-subst
+datahipy/_version.py export-subst

.github/workflows/documentation.yml

@@ -8,7 +8,7 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: '3.9'
-      - name: Install bids_tools and dependencies
+      - name: Install datahipy and dependencies
         run: |
           pip install -r docs/requirements.txt
           pip install -e .[all]

.gitlab-ci.yml

@@ -13,6 +13,7 @@ variables:
   REG_VERSION: 0.16.1
   GL_TOKEN: $GL_TOKEN
   GH_TOKEN: $GH_TOKEN
+  SSH_PRIVATE_KEY: $SSH_PRIVATE_KEY
 services:
   - name: docker:20-dind
     alias: docker
@@ -40,8 +41,24 @@ before_script:
   - curl --fail --show-error --location "https://github.com/genuinetools/reg/releases/download/v$REG_VERSION/reg-linux-amd64" --output ./reg
   - echo "$REG_SHA256  ./reg" | sha256sum -c -
   - chmod a+x ./reg
+  # install additional dependencies required by codecov uploader
+  - apk add --no-cache gnupg coreutils
   # login the gitlab container registry
   - echo $CI_REGISTRY_PASSWORD | docker login $CI_REGISTRY -u $CI_REGISTRY_USER --password-stdin
+  # install ssh-agent if not already installed, it is required by Docker
+  - 'command -v ssh-agent >/dev/null || ( apt-get update -y && apt-get install openssh-client -y )'
+  # run ssh-agent (inside the build environment)
+  - eval $(ssh-agent -s)
+  # create the SSH directory and give it the right permissions
+  - mkdir -p ~/.ssh
+  - chmod 700 ~/.ssh
+  # give the right permissions, otherwise ssh-add will refuse to add files
+  - echo "$SSH_PRIVATE_KEY" > ~/.ssh/id_gitlab_rsa
+  - chmod 400 ~/.ssh/id_gitlab_rsa
+  # add github to the list of known host
+  - ssh-keyscan -H github.com >> ~/.ssh/known_hosts
+  # add the SSH key stored in SSH_PRIVATE_KEY file type CI/CD variable to the agent store
+  - ssh-add ~/.ssh/id_gitlab_rsa
 
 stages:
   - test-python-install
@@ -55,13 +72,23 @@ test:
   stage: test
   needs: ["build"]
   script:
+    # Run tests
     - make test TAG=$(python get_version.py)-dev.${CI_COMMIT_REF_NAME}
-  coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
-  artifacts:
-    reports:
-      coverage_report:
-        coverage_format: cobertura
-        path: test/report/cov.xml
+    # Download codecov uploader with integrity check
+    # - curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --no-default-keyring --keyring trustedkeys.gpg --import
+    - curl -Os https://uploader.codecov.io/latest/alpine/codecov
+    # - curl -Os https://uploader.codecov.io/latest/alpine/codecov.SHA256SUM
+    # - curl -Os https://uploader.codecov.io/latest/alpine/codecov.SHA256SUM.sig
+    # - gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
+    - chmod +x codecov
+    # Upload the coverage report to codecov
+    - ./codecov -t ${CODECOV_TOKEN} --file test/report/cov.xml
+      
+  # artifacts:
+  #   reports:
+  #     coverage_report:
+  #       coverage_format: cobertura
+  #       path: test/report/cov.xml
 
 test-python-install:
   stage: test-python-install
@@ -107,7 +134,8 @@ deploy-release:
     - make build-docker TAG=$(python get_version.py)
     - make push-docker-ci TAG=$(python get_version.py)
     # Add our Github remote repository and fined-grained token authentication
-    - git remote add github_origin "https://oauth2:$GH_TOKEN@github.com/HIP-infrastructure/bids-tools"
+    - echo "GH_TOKEN=${GH_TOKEN}"
+    - GH_TOKEN=${GH_TOKEN} git remote add github_origin git@github.com:HIP-infrastructure/datahipy.git
     # Push commits created by semantic-release for version change and changelog
     - git push github_origin $CI_COMMIT_REF_NAME
     # Push the new tag created by semantic-release

.releaserc.json

@@ -14,18 +14,10 @@
         "replacements": [
           {
             "files": [
-              "bids_tools/info.py"
+              "datahipy/info.py"
             ],
             "from": "__version__ = \".*\"",
             "to": "__version__ = \"${nextRelease.version}\"",
-            "results": [
-              {
-                "file": "bids_tools/info.py",
-                "hasChanged": true,
-                "numMatches": 1,
-                "numReplacements": 1
-              }
-            ],
             "countMatches": true
           }
         ]
@@ -50,7 +42,7 @@
       "@semantic-release/git",
       {
         "assets": [
-          "bids_tools/info.py",
+          "datahipy/info.py",
           "docs/CHANGES.md"
         ],
         "message": "chore(release): ${nextRelease.version} [skip ci]\n\n${nextRelease.notes}"

Dockerfile

@@ -104,23 +104,23 @@ RUN pip3 install \
     rm -rf /var/lib/apt/lists/*
 
 ###############################################################################
-# Install bids-tools
+# Install datahipy
 ###############################################################################
 
-# Set the working directory to /app/bids_tools
-WORKDIR /apps/bids_tools
+# Set the working directory to /app/datahipy
+WORKDIR /apps/datahipy
 
 # Copy necessary contents of this repository.
 COPY ./.coveragerc ./.coveragerc
 COPY setup.py ./setup.py
 COPY setup.cfg ./setup.cfg
 COPY README.md ./README.md
-COPY bids_tools ./bids_tools
+COPY datahipy ./datahipy
 # COPY LICENSE ./LICENSE
 
-# Install bids-tools with static version taken from the argument
+# Install datahipy with static version taken from the argument
 ARG VERSION=unknown
-RUN echo "${VERSION}" > /apps/bids_tools/bids_tools/VERSION \
+RUN echo "${VERSION}" > /apps/datahipy/datahipy/VERSION \
     && pip install -e ".[test]"
 
 ###############################################################################
@@ -174,15 +174,15 @@ LABEL org.label-schema.build-date=${BUILD_DATE} \
     org.label-schema.docker.cmd="docker run --rm \
     -v /path/to/dataset:/output \
     -v /path/to/input:/input \
-    bids-tools \
+    datahipy \
     USERNAME USERID \
     [--command {dataset.create,dataset.get,datasets.get,sub.get,sub.import,sub.edit.clinical,sub.delete,sub.delete.file}] \
     [--input_data /input/input_data.json] [--output_file /input/output_data.json] \
     [--dataset_path /output] [--input_path /input]" \
     org.label-schema.docker.cmd.test="docker run --rm \
     --entrypoint /entrypoint_pytest.sh \
-    -v /path/to/bids-tools/test:/test \
-    -v /path/to/bids-tools/bids_tools:/apps/bids_tools/bids_tools \
-    bids-tools \
+    -v /path/to/datahipy/test:/test \
+    -v /path/to/datahipy/datahipy:/apps/datahipy/datahipy \
+    datahipy \
     USERNAME USERID \
     /test"

Makefile

@@ -14,7 +14,7 @@ override TAG := $(subst _,-,$(TAG))
 $(info TAG (Normalized) = $(TAG))
 
 # Define the complete docker image tag 
-IMAGE_TAG = $(if $(CI_REGISTRY),$(CI_REGISTRY)/hip/bids-tools:$(TAG),bids-tools:$(TAG)) 
+IMAGE_TAG = $(if $(CI_REGISTRY),$(CI_REGISTRY)/hip/datahipy:$(TAG),datahipy:$(TAG)) 
 
 # Define the build date and vcs reference
 BUILD_DATE = $(shell date -u +"%Y-%m-%dT%H:%M:%SZ")
@@ -34,14 +34,14 @@ test:
 	docker run -t --rm \
 		--entrypoint "/entrypoint_pytest.sh" \
 		-v $(PROJECT_DIR)/test:/test \
-		-v $(PROJECT_DIR)/bids_tools:/apps/bids_tools/bids_tools \
+		-v $(PROJECT_DIR)/datahipy:/apps/datahipy/datahipy \
 		$(IMAGE_TAG) \
 		$(USER) \
 		$(USER_ID) \
 		/test
 	@echo "Fix path in coverage xml report..."
 	sed -i -r  \
-		"s|/apps/bids_tools/bids_tools|$(PROJECT_DIR)/bids_tools|g" \
+		"s|/apps/datahipy/datahipy|$(PROJECT_DIR)/datahipy|g" \
 		$(PROJECT_DIR)/test/report/cov.xml
 
 #build-docker: @ Builds the Docker image
@@ -54,7 +54,7 @@ build-docker:
 
 #push-docker-ci: @ Push the Docker image with TAG to the CI registry
 push-docker-ci:
-	docker push $(CI_REGISTRY)/hip/bids-tools:$(TAG)
+	docker push $(CI_REGISTRY)/hip/datahipy:$(TAG)
 
 #rm-docker-ci: @ Remove the Docker image with TAG to the CI registry
 # from https://docs.gitlab.com/ee/user/packages/container_registry/delete_container_registry_images.html#use-gitlab-cicd
@@ -71,7 +71,7 @@ install-python:
 
 #install-python-wheel: @ Installs the python wheel
 install-python-wheel: build-python-wheel
-	pip install bids_tools
+	pip install datahipy
 
 #build-python-wheel: @ Builds the python wheel
 build-python-wheel:
@@ -79,7 +79,7 @@ build-python-wheel:
 
 #test-python-install: @ Tests the python package installation
 test-python-install: install-python install-python-wheel	
-	bids_tools --version
+	datahipy --version
 
 #help:	@ List available tasks on this project
 help:

README.md

-# `bids_tools`: Tools to manage BIDS datasets in the Human intracranial EEG platform
+# ![DataHIPy logo](https://raw.githubusercontent.com/HIP-infrastructure/datahipy/chore/update-tool-name-and-logo/docs/logos/datahipy-logo-text.png)
 
-Copyright © 2012-2023 The HIP team and Contributors, All rights reserved.
+Copyright © 2022-2023 The HIP team, University Hospital of Lausanne (CHUV), Switzerland & Contributors, All rights reserved.
 
 This software is distributed under the open-source Apache 2.0 license. See [LICENSE](LICENSE.txt) file for details.
 
 ---
 
-![Latest GitHub Release](https://img.shields.io/github/v/release/HIP-infrastructure/bids-tools?include_prereleases) ![Latest GitHub Release Date](https://img.shields.io/github/release-date-pre/HIP-infrastructure/bids-tools) [![CI/CD](https://gitlab.hbp.link/hip/bids-tools/badges/master/pipeline.svg)](https://gitlab.hbp.link/hip/bids-tools/-/commits/master) [![Coverage](https://gitlab.hbp.link/hip/bids-tools/badges/master/coverage.svg)](https://gitlab.hbp.link/hip/bids-tools/-/commits/master)
+![Latest GitHub Release](https://img.shields.io/github/v/release/HIP-infrastructure/datahipy?include_prereleases) ![Latest GitHub Release Date](https://img.shields.io/github/release-date-pre/HIP-infrastructure/datahipy) [![Digital Object Identifier (DOI)](https://zenodo.org/badge/428721094.svg)](https://zenodo.org/badge/latestdoi/428721094) [![CI/CD](https://gitlab.hbp.link/hip/datahipy/badges/master/pipeline.svg?private_token=glpat-a_qxRwZSNcAq9CMoK2tA)](https://gitlab.hbp.link/hip/datahipy/-/commits/master) [![codecov](https://codecov.io/github/HIP-infrastructure/datahipy/branch/master/graph/badge.svg?token=F1CWBIGXJN)](https://codecov.io/github/HIP-infrastructure/datahipy)
 
-`bids_tools` is an open-source tool written in Python and encapsulated in a Docker image to handle neuroimaging data on the Human Intracranial EEG Platform (HIP) following Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io)).
+`DataHIPy` is an open-source tool written in Python and encapsulated in a Docker image to handle neuroimaging data on the Human Intracranial EEG Platform (HIP) following Brain Imaging Data Structure ([BIDS](https://bids-specification.readthedocs.io)).
 
 ### Resources
 
-*   **Documentation:** https://hip-infrastructure.github.io/bids-tools/
-*   **Source:** https://github.com/HIP-infrastructure/bids-tools
-*   **Bug reports:** https://github.com/HIP-infrastructure/bids-tools/issues
+*   **Documentation:** https://hip-infrastructure.github.io/datahipy/
+*   **Source:** https://github.com/HIP-infrastructure/datahipy
+*   **Bug reports:** https://github.com/HIP-infrastructure/datahipy/issues
 
 ## Installation
 
-*   Install Docker engine (See [instructions](https://hip-infrastructure.github.io/bids-tools/installation.html#installation-of-docker-engine))
+*   Install Docker engine (See [instructions](https://hip-infrastructure.github.io/datahipy/installation.html#installation-of-docker-engine))
 
-*   Clone this repository and go to the `bids-tools` directory:
+*   Clone this repository and go to the `datahipy` directory:
 
     ```bash
-    $ git clone https://github.com/HIP-infrastructure/bids-tools.git
-    $ cd bids-tools
+    $ git clone https://github.com/HIP-infrastructure/DataHIPy.git
+    $ cd DataHIPy
     ```
 
 *   Checkout submodules:
@@ -39,7 +39,7 @@ This software is distributed under the open-source Apache 2.0 license. See [LICE
     $ make -B build-docker
     ```
 
-*   You are ready to use `bids_tools` :rocket:!
+*   You are ready to use `DataHIPy` :rocket:!
 
 ## Test
 Run `test/run_tests.sh` in a terminal:
@@ -53,7 +53,7 @@ After completion, coverage report in HTML format can be found in ``test/report/c
 The tool can be easily run as follows:
 
 ```output
-usage: bids_tools [-h]
+usage: datahipy [-h]
                   [--command {dataset.create,dataset.get,datasets.get,sub.get,sub.import,sub.edit.clinical,sub.delete,sub.delete.file}]
                   [--input_data INPUT_DATA]
                   [--output_file OUTPUT_FILE]

bids_tools/__init__.py → datahipy/__init__.py

-from bids_tools.info import (
+from datahipy.info import (
     __version__,
     __author__,
     __email__,

bids_tools/bids/bids_manager.py → datahipy/bids/bids_manager.py

@@ -7,7 +7,7 @@ import os
 import re
 import json
 
-from bids_tools.bids.dataset import create_bids_layout
+from datahipy.bids.dataset import create_bids_layout
 
 
 def post_import_bids_refinement(bids_dir):

bids_tools/bids/const.py → datahipy/bids/const.py

 # Copyright (C) 2022-2023, The HIP team and Contributors, All rights reserved.
 #  This software is distributed under the open-source Apache 2.0 license.
 
-"""Define constants used by packages of `bids_tools.bids`."""
+"""Define constants used by packages of `datahipy.bids`."""
 
 BIDS_VERSION = "v1.7.0"
 

bids_tools/bids/dataset.py → datahipy/bids/dataset.py

@@ -9,16 +9,17 @@ import subprocess
 from concurrent.futures import ProcessPoolExecutor
 from pkg_resources import resource_filename
 from sre_constants import SUCCESS
+from datetime import date
 
 from bids import BIDSLayout
 
-from bids_tools.bids.electrophy import get_ieeg_info
-from bids_tools.bids.participant import get_participants_info
-from bids_tools.bids.validation import (
+from datahipy.bids.electrophy import get_ieeg_info
+from datahipy.bids.participant import get_participants_info
+from datahipy.bids.validation import (
     add_bidsignore_validation_rule,
     get_bids_validator_output_info,
 )
-from bids_tools.bids.version import determine_bids_schema_version
+from datahipy.bids.version import determine_bids_schema_version
 
 
 # Set the number of threads to use for parallel processing
@@ -27,6 +28,86 @@ from bids_tools.bids.version import determine_bids_schema_version
 NUM_THREADS = os.cpu_count() - 1 if os.cpu_count() > 1 else 1
 
 
+def create_initial_bids_readme(bids_dir, dataset_desc):
+    """Create an initial `README` file for a BIDS dataset.
+
+    Parameters
+    ----------
+    bids_dir : str
+        Path to the BIDS dataset.
+
+    dataset_desc : dict
+        Dictionary with the content of the dataset_description.json file.
+    """
+    with open(os.path.join(bids_dir, "README"), "w") as f:
+        f.writelines(
+            [
+                f'# {dataset_desc["Name"]}\n\n',
+                f"To be completed...\n\n",
+                f"Use it as the dataset landing page, "
+                "which should provide enough information "
+                "about the dataset and its creation context.",
+            ]
+        )
+
+
+def create_initial_bids_changes(bids_dir):
+    """Create an initial `CHANGES` file for a BIDS dataset.
+
+    Parameters
+    ----------
+    bids_dir : str
+        Path to the BIDS dataset.
+    """
+    with open(os.path.join(bids_dir, "CHANGES"), "w") as f:
+        f.writelines(
+            [
+                f"0.0.0 {date.today().strftime('%Y-%m-%d')}\n",
+                "\t- Creation of the dataset.",
+            ]
+        )
+
+
+def create_initial_participants_tsv(bids_dir):
+    """Create an initial `participants.tsv` file for a BIDS dataset.
+
+    Parameters
+    ----------
+    bids_dir : str
+        Path to the BIDS dataset.
+    """
+    with open(os.path.join(bids_dir, "participants.tsv"), "w") as f:
+        f.write("participant_id\tage\tsex\tgroup")
+
+
+def create_empty_bids_dataset(bids_dir=None, dataset_desc=None):
+    """Create an empty BIDS dataset.
+
+    Parameters
+    ----------
+    bids_dir : str
+        Path to the BIDS dataset.
+
+    dataset_desc : dict
+        Dictionary with the content of the dataset_description.json file.
+    """
+    print("> Creating an empty BIDS dataset at: ", bids_dir, "...")
+    # Create the BIDS dataset directory
+    os.makedirs(bids_dir, exist_ok=True)
+    # Create the dataset_description.json file
+    with open(os.path.join(bids_dir, "dataset_description.json"), "w") as f:
+        json.dump(dataset_desc, f, indent=4)
+    # Create initial README file
+    create_initial_bids_readme(bids_dir, dataset_desc)
+    # Create initial CHANGES file
+    create_initial_bids_changes(bids_dir)
+    # Create the .bidsignore file and add the line to ignore CT files
+    # (not yet supported by the validator)
+    add_bidsignore_validation_rule(bids_dir, "**/*_ct.*")
+    # Create an initial participants.tsv file
+    create_initial_participants_tsv(bids_dir)
+
+
 def create_bids_layout(bids_dir=None, **kwargs):
     """Create a pybids representation of a BIDS dataset.
 
@@ -47,7 +128,7 @@ def create_bids_layout(bids_dir=None, **kwargs):
     layout = BIDSLayout(
         root=bids_dir,
         validate=False,
-        config=resource_filename("bids_tools", "bids/config/bids.json"),
+        config=resource_filename("datahipy", "bids/config/bids.json"),
         **kwargs,
     )
     return layout
@@ -101,9 +182,7 @@ def get_dataset_size(bids_dir=None):
     """
     # Get total number of files and size
     total_size_megabytes = (
-        subprocess.check_output(["du", "-sh", bids_dir])
-        .split()[0]
-        .decode("utf-8")
+        subprocess.check_output(["du", "-sh", bids_dir]).split()[0].decode("utf-8")
     )
     ## Alternative: Count only files outside sourcedata/
     # total_size_bytes = 0
@@ -146,9 +225,7 @@ def get_bidsdataset_content(bids_dir=None):
     add_bidsignore_validation_rule(bids_dir, "**/*_ct.*")
     # Run the bids-validator on the dataset with the specified schema version and
     # update dataset_desc with the execution dictionary output
-    dataset_desc.update(
-        get_bids_validator_output_info(bids_dir, bids_schema_version)
-    )
+    dataset_desc.update(get_bids_validator_output_info(bids_dir, bids_schema_version))
     # Add information retrieved with pybids to dataset_desc
     dataset_desc.update(get_bids_layout_info(bids_dir))
     # Return the created dataset_desc dictionary to be indexed

bids_tools/bids/participant.py → datahipy/bids/participant.py

@@ -5,7 +5,7 @@
 
 import pandas as pd
 from os import path as op
-from bids_tools.bids.const import (
+from datahipy.bids.const import (
     VALID_EXTENSIONS,
     BIDS_ENTITY_MAP,
     BIDSJSONFILE_DATATYPE_KEY_MAP,
@@ -30,8 +30,8 @@ def get_subject_bidsfile_info(bids_dir, **kwargs):
         List of dictionaries with BIDS file information for a given subject.
     """
     # Import the required functions
-    from bids_tools.bids.dataset import create_bids_layout
-    from bids_tools.bids.electrophy import get_channels_info
+    from datahipy.bids.dataset import create_bids_layout
+    from datahipy.bids.electrophy import get_channels_info
 
     # Create a pybids representation of the dataset
     layout = create_bids_layout(bids_dir)

bids_tools/bids/validation.py → datahipy/bids/validation.py

@@ -6,7 +6,7 @@
 import json
 import subprocess
 from os import path as op
-from bids_tools.bids.const import BIDS_VERSION
+from datahipy.bids.const import BIDS_VERSION
 
 
 def validate_bids_dataset(container_dataset_path, *args):

bids_tools/bids/version.py → datahipy/bids/version.py

@@ -4,7 +4,7 @@
 """Utility functions to retrieve version related information from a BIDS dataset."""
 
 from packaging import version
-from bids_tools.bids.const import BIDS_VERSION
+from datahipy.bids.const import BIDS_VERSION
 
 
 def determine_bids_schema_version(dataset_desc):