updates to init

.github/workflows/cd.yaml

@@ -1,15 +1,15 @@
 name: Continuous Deployment
 
 on:
-  release:
-    types: [created]
+  workflow_dispatch:
+
 
 jobs:
   run_redundant_test:
     runs-on: ubuntu-latest
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
 
     - name: Set up Python
       uses: actions/setup-python@v2
@@ -21,21 +21,52 @@ jobs:
         python -m pip install --upgrade pip
         pip install -r requirements.txt
 
-    # - name: Test BioCompose API
-    #   run: |
-    #     pytest
-
   release_new_version:
     needs: run_redundant_test
     runs-on: ubuntu-latest
     steps:
     - name: Checkout code
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.10'  # Set the Python version you need
+
+    - name: Install make
+      run: |
+        sudo apt-get update 
+        sudo apt-get install -y make 
+
+    - name: Install Poetry
+      run: |
+        curl -sSL https://install.python-poetry.org | python3 -
+        echo "export PATH=$HOME/.local/bin:$PATH" >> $GITHUB_ENV
+        source $GITHUB_ENV
+
+    - name: Install dependencies
+      run: |
+        poetry install
+
+    - name: Extract project version
+      run: |
+        VERSION=$(python -c "import toml; print(toml.load('pyproject.toml')['tool']['poetry']['version'])")
+        echo "VERSION=$VERSION" >> $GITHUB_ENV
+
+    - name: Build Documentation
+      run: |
+        make -C documentation clean
+        make -C documentation html
+
+    - name: Create new github tags
+      run: |
+        git tag -m ${{ env.VERSION }}
+        git push --tags
 
-    - name: Release new version on PyPI
+    - name: Publish new version on PyPI
       run: |
-        echo "Run pypi_release.sh here"
-      # run: ./push.sh
+        poetry build
+        poetry publish --username __token__ --password ${{ secrets.ADMIN_PYPI_TOKEN }}
 
     - name: Notify Deployment
-      run: echo "Deployment successful on release ${{ github.ref }}"
+      run: echo "Version ${{ env.VERSION }} as been published on PyPI with release ${{ github.ref }}"

bio_compose/__init__.py

@@ -1,177 +1,12 @@
 import os
 
+import toml
+
 from bio_compose.api import *
 
 
 current_dir = os.path.dirname(__file__)
-version_file_path = os.path.join(current_dir, '_VERSION')
-
-
-with open(version_file_path, 'r') as f:
-    __version__ = f.read().strip()
-
+repo_root = os.path.abspath(os.path.join(current_dir, '..'))
+pyproject_file_path = os.path.join(repo_root, 'pyproject.toml')
 
-# def run_simulation(*args, **kwargs) -> SimulationResult:
-#     """Run a simulation with BioCompose.
-#
-#     :param args: Positional arguments
-#
-#     * 1 argument: smoldyn simulation configuration in which time parameters (dt, duration) are already defined. **Smoldyn simulation only**.
-#     * 3 arguments: smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt. **Smoldyn simulation only**.
-#     * 5 arguments: sbml filepath, simulation start, simulation end, simulation steps, simulator. **SBML simulation only**.
-#
-#     :param kwargs: Keyword arguments
-#
-#     :return: instance of simulation results.
-#     :rtype: bio_compose.runner.SimulationResult
-#     """
-#     # set up submission
-#     runner = SimulationRunner()
-#     in_file = args[0]
-#     n_args = len(args)
-#     submission = None
-#
-#     if n_args == 1:
-#         submission = runner.run_smoldyn_simulation(smoldyn_configuration_filepath=in_file)
-#     elif n_args == 3:
-#         dur = args[1]
-#         dt = args[2]
-#         submission = runner.run_smoldyn_simulation(smoldyn_configuration_filepath=in_file, duration=dur, dt=dt)
-#     elif n_args == 5:
-#         start = args[1]
-#         end = args[2]
-#         steps = args[3]
-#         simulator = args[4]
-#         submission = runner.run_utc_simulation(sbml_filepath=in_file, start=start, end=end, steps=steps, simulator=simulator)
-#
-#     # fetch result params
-#     job_id = submission.get('job_id')
-#     output = {}
-#     timeout = kwargs.get('timeout', 100)
-#
-#     # poll gateway for results
-#     i = 0
-#     if job_id is not None:
-#         print(f'Submission Results for Job ID {job_id}: ')
-#         while True:
-#             if i == timeout:
-#                 break
-#             simulation_result = runner.get_output(job_id=job_id)
-#             if isinstance(simulation_result, dict):
-#                 status = simulation_result['content']['status']
-#                 last4 = get_job_signature(job_id)
-#                 if not 'COMPLETED' in status:
-#                     print(f'Status for job ending in {last4}: {status}')
-#                     i += 1
-#                     time.sleep(1)
-#                 else:
-#                     output = simulation_result
-#                     break
-#             else:
-#                 i += 1
-#
-#     return SimulationResult(data=output)
-#
-#
-# def verify(*args, **kwargs) -> VerificationResult:
-#     """Verify and compare the outputs of simulators for a given entrypoint file of either sbml or omex.
-#
-#     :param args: Positional arguments
-#
-#     * 1 argument: submit omex verification with no time params. **OMEX verification only**.
-#     * 2 arguments: omex filepath, simulators to include in the verification. **OMEX verification only**.
-#     * 4 arguments: sbml filepath, start, stop, steps. **SBML verification only**.
-#     * 5 arguments: sbml filepath, start, stop, steps, simulators. **SBML verification only**.
-#
-#     :param kwargs: keyword arguments passed to the verification.
-#
-#     * keyword arguments either of the `bio_compose.verifier.Verifier.verify_...` methods. See verifier module documentation for more details.
-#     * timeout: (`int`) number of iterations to perform polling before function halts. Defaults to 50
-#     * buffer_time: (`Union[int, float]`) initial buffer time of data-fetching. Defaults to 5
-#     * poll_time: (`Union[int, float]`) poll time of data-fetching which is applied if the result is not yet ready.
-#     * verbose: (`bool`) whether to print status updates to stdout. Defaults to True.
-#
-#     :return: instance of verification results.
-#     :rtype: bio_compose.runner.VerificationResult
-#     """
-#     verifier = Verifier()
-#     if len(args) == 2:
-#         simulators = args[1]
-#     else:
-#         simulators = kwargs.get('simulators')
-#     run_sbml = False
-#     for arg in args:
-#         if isinstance(arg, int):
-#             run_sbml = True
-#     submission = None
-#
-#     # parse executor
-#     if run_sbml:
-#         submission = verifier.verify_sbml(*args, **kwargs)
-#     else:
-#         submission = verifier.verify_omex(*args, **kwargs)
-#
-#     # fetch params
-#     job_id = submission.get('job_id')
-#     timeout = kwargs.get('timeout', 50)
-#     buffer_time = kwargs.get('buffer_time', 5)
-#     poll_time = kwargs.get('poll_time', 5)
-#     verbose = kwargs.get('verbose', True)
-#
-#     # poll gateway for results
-#     n_attempts = 0
-#     output = {}
-#     if job_id is not None:
-#         # submit request and buffer
-#         verification_result = verifier.get_output(job_id=job_id)
-#         msg = ''
-#         for _ in range(buffer_time):
-#             msg += '='
-#             print("Submitting verification " + msg + ">", end='\r') if verbose else None
-#             time.sleep(0.2)
-#
-#         # confirm submission
-#         complete = "".join(["=" for _ in range(buffer_time)])
-#         time.sleep(0.2)
-#         initial_status = verification_result.get('content', {}).get('status', '')
-#         if initial_status.startswith("SUBMITTED"):
-#             print("Submitting verification " + complete + ">" + f" verification submitted!\n") if verbose else None
-#             print(f"VERIFICATION JOB ID:\n{job_id}\n") if verbose else None
-#             time.sleep(0.5)
-#
-#         # set output data from result data if it is ready, otherwise sleep and reiterate
-#         current_status = verifier.get_output(job_id=job_id).get('content', {}).get('status', '')
-#         # polling loop
-#         while True:
-#             # dynamic message render
-#             status_message = f'Status for job ending in {get_job_signature(job_id)}: {current_status} '
-#             message = ''
-#             if not "COMPLETED" in current_status or "FAILED" in current_status:
-#                 for _ in range(poll_time * 4):
-#                     print("".join([" " for _ in message]), end='\r') if verbose else None
-#                     message += '='
-#                     print("Running verification " + message + ">", end='\r') if verbose else None
-#                     time.sleep(0.1)
-#                 message += ">"
-#                 print(f'Running verification {message} {status_message}') if verbose else None
-#             else:
-#                 print(f'\nVerification complete!') if verbose else None
-#                 output = verifier.get_output(job_id=job_id)
-#                 break
-#
-#             if 'FAILED' in current_status:
-#                 output = {}
-#                 break
-#
-#             if not 'COMPLETED' in current_status:
-#                 # quit iteration if timeout is reached
-#                 if n_attempts == timeout:
-#                     break
-#                 # iteration
-#                 n_attempts += 1
-#                 current_status = verifier.get_output(job_id=job_id).get('content', {}).get('status', '')
-#             else:
-#                 output = verifier.get_output(job_id=job_id)
-#                 break
-#
-#     return VerificationResult(data=output)
+__version__ = toml.load('pyproject.toml')['tool']['poetry']['version']

bio_compose/api.py

@@ -33,7 +33,11 @@ def verify(*args) -> VerificationResult:
     :return: instance of verification results.
     :rtype: bio_compose.verifier.VerificationResult
     """
-    verifier = Verifier()
+    verifier = API_VERIFIER
+
+    if len(args) == 0:
+        raise ValueError('At least one positional argument defining a file entrypoint is required.')
+
     if len(args) == 2:
         simulators = args[1]
     elif len(args) == 5:
@@ -88,3 +92,60 @@ def verify(*args) -> VerificationResult:
                 break
 
     return VerificationResult(data=output)
+
+
+def run_simulation(*args, **kwargs) -> SimulationResult:
+    """Run a simulation with BioCompose.
+
+    :param args: Positional arguments
+    * 1 argument: smoldyn simulation configuration in which time parameters (dt, duration) are already defined. **Smoldyn simulation only**.
+    * 3 arguments: smoldyn configuration file, smoldyn simulation duration, smoldyn simulation dt. **Smoldyn simulation only**.
+    * 5 arguments: sbml filepath, simulation start, simulation end, simulation steps, simulator. **SBML simulation only**.
+
+    :param kwargs: Keyword arguments
+
+    :return: instance of simulation results.
+    :rtype: bio_compose.runner.SimulationResult
+    """
+    # set up submission
+    runner = SimulationRunner()
+    in_file = args[0]
+    n_args = len(args)
+    submission = None
+    if n_args == 1:
+        submission = runner.run_smoldyn_simulation(smoldyn_configuration_filepath=in_file)
+    elif n_args == 3:
+        dur = args[1]
+        dt = args[2]
+        submission = runner.run_smoldyn_simulation(smoldyn_configuration_filepath=in_file, duration=dur, dt=dt)
+    elif n_args == 5:
+        start = args[1]
+        end = args[2]
+        steps = args[3]
+        simulator = args[4]
+        submission = runner.run_utc_simulation(sbml_filepath=in_file, start=start, end=end, steps=steps, simulator=simulator)
+    # fetch result params
+    job_id = submission.get('job_id')
+    output = {}
+    timeout = kwargs.get('timeout', 100)
+    # poll gateway for results
+    i = 0
+    if job_id is not None:
+        print(f'Submission Results for Job ID {job_id}: ')
+        while True:
+            if i == timeout:
+                break
+            simulation_result = runner.get_output(job_id=job_id)
+            if isinstance(simulation_result, dict):
+                status = simulation_result['content']['status']
+                last4 = get_job_signature(job_id)
+                if not 'COMPLETED' in status:
+                    print(f'Status for job ending in {last4}: {status}')
+                    i += 1
+                    time.sleep(1)
+                else:
+                    output = simulation_result
+                    break
+            else:
+                i += 1
+    return SimulationResult(data=output)

pyproject.toml

@@ -17,6 +17,7 @@ requests-toolbelt = "^1.0.0"
 seaborn = "^0.13.2"
 antimony = "^2.15.0"
 process-bigraph = "^0.0.19"
+toml = "^0.10.2"
 
 [tool.poetry.group.dev.dependencies]
 pytest = "^8.3.2"

scripts/pypi_release.sh

@@ -42,9 +42,6 @@ if [ ! -z "$(git status --untracked-files=no --porcelain)" ]; then
     exit 1
 fi
 
-# update internal version
-echo "$version" > ./bio_compose/_VERSION
-
 # update documentation
 # ./scripts/update_docs.sh
 cd documentation || exit 1