From e8301f9c81ff838b11936ead15629b77f8e2c24d Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 2 Apr 2024 14:50:12 +0200
Subject: [PATCH 01/20] Clean up and fix logging

---
 src/hermes/commands/cli.py |  3 +++
 src/hermes/logger.py       | 16 +++++-----------
 2 files changed, 8 insertions(+), 11 deletions(-)

diff --git a/src/hermes/commands/cli.py b/src/hermes/commands/cli.py
index e13cfcf0..5ca827de 100644
--- a/src/hermes/commands/cli.py
+++ b/src/hermes/commands/cli.py
@@ -10,6 +10,7 @@
 """
 import argparse
 
+from hermes import logger
 from hermes.commands import HermesHelpCommand, HermesCleanCommand, HermesHarvestCommand, HermesProcessCommand, \
                             HermesCurateCommand, HermesDepositCommand, HermesPostprocessCommand
 from hermes.commands.base import HermesCommand
@@ -56,6 +57,8 @@ def main() -> None:
     # Actually parse the command line, configure it and execute the selected sub-command.
     args = parser.parse_args()
 
+    logger.init_logging()
+
     args.command.load_settings(args)
     args.command.patch_settings(args)
     args.command(args)
diff --git a/src/hermes/logger.py b/src/hermes/logger.py
index cd8b28bc..7b6dd981 100644
--- a/src/hermes/logger.py
+++ b/src/hermes/logger.py
@@ -31,7 +31,7 @@
             'class': "logging.FileHandler",
             'formatter': "logfile",
             'level': "DEBUG",
-            'filename': "./.hermes/hermes.log",
+            'filename': "./hermes.log",
         },
 
         'auditfile': {
@@ -50,12 +50,6 @@
     },
 }
 
-# This dict caches all the different configuration sections already loaded
-_config = {
-    # We need some basic logging configuration to get logging up and running at all
-    'logging': _logging_config,
-}
-
 _loggers = {}
 
 
@@ -64,14 +58,14 @@ def init_logging():
         return
 
     # Make sure the directories to hold the log files exists (or else create)
-    pathlib.Path(_config['logging']['handlers']['logfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
-    pathlib.Path(_config['logging']['handlers']['auditfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
+    pathlib.Path(_logging_config['handlers']['logfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
+    pathlib.Path(_logging_config['handlers']['auditfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
 
     # Inintialize logging system
     import logging.config
 
-    logging.config.dictConfig(_config['logging'])
-    for log_name in _config['logging']['loggers']:
+    logging.config.dictConfig(_logging_config)
+    for log_name in _logging_config['loggers']:
         _loggers[log_name] = logging.getLogger(log_name)
 
 

From fb918f83a57107ce282735dff8f59a8f857a471d Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 2 Apr 2024 14:53:17 +0200
Subject: [PATCH 02/20] Remove debug print statements

---
 src/hermes/commands/deposit/base.py | 1 -
 src/hermes/commands/harvest/base.py | 6 ++----
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/src/hermes/commands/deposit/base.py b/src/hermes/commands/deposit/base.py
index e92249ad..5f0290c2 100644
--- a/src/hermes/commands/deposit/base.py
+++ b/src/hermes/commands/deposit/base.py
@@ -120,7 +120,6 @@ def init_command_parser(self, command_parser: argparse.ArgumentParser) -> None:
     def __call__(self, args: argparse.Namespace) -> None:
         self.args = args
         plugin_name = self.settings.target
-        print(self.args)
 
         ctx = CodeMetaContext()
         codemeta_file = ctx.get_cache("curate", ctx.hermes_name)
diff --git a/src/hermes/commands/harvest/base.py b/src/hermes/commands/harvest/base.py
index dee745c5..629342e7 100644
--- a/src/hermes/commands/harvest/base.py
+++ b/src/hermes/commands/harvest/base.py
@@ -48,10 +48,8 @@ def __call__(self, args: argparse.Namespace) -> None:
             try:
                 plugin_func = self.plugins[plugin_name]()
                 harvested_data, tags = plugin_func(self)
-                print(harvested_data)
-                with HermesHarvestContext(
-                        ctx, plugin_name
-                ) as harvest_ctx:
+
+                with HermesHarvestContext(ctx, plugin_name) as harvest_ctx:
                     harvest_ctx.update_from(harvested_data,
                                             plugin=plugin_name,
                                             timestamp=datetime.now().isoformat(), **tags)

From 7a4aa40de40c62d644753b28a82636dac2ddba08 Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Thu, 4 Apr 2024 10:34:15 +0200
Subject: [PATCH 03/20] Start re-activating and adding some tests

---
 test/hermes_test/conftest.py |  2 ++
 test/hermes_test/test_cli.py | 10 +++++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/test/hermes_test/conftest.py b/test/hermes_test/conftest.py
index 16f3b7a0..2d3e52b2 100644
--- a/test/hermes_test/conftest.py
+++ b/test/hermes_test/conftest.py
@@ -23,8 +23,10 @@ def __setitem__(self, path, data):
 
     def __enter__(self):
         self.test_path.mkdir(parents=True, exist_ok=True)
+
         for file_name, data in self.test_files.items():
             file_path = self.test_path / file_name
+            file_path.parent.mkdir(parents=True, exist_ok=True)
             file_path.write_text(data)
 
         os.chdir(self.test_path)
diff --git a/test/hermes_test/test_cli.py b/test/hermes_test/test_cli.py
index 9261c391..85b40e5e 100644
--- a/test/hermes_test/test_cli.py
+++ b/test/hermes_test/test_cli.py
@@ -9,23 +9,27 @@
 from hermes.commands import cli
 
 
-def test_hermes_full(capsys):
+def test_hermes_full():
     with pytest.raises(SystemExit) as se:
         cli.main()
         assert "choose from" in se
 
 
-@pytest.mark.skip(reason="Needs update")
 def test_hermes_harvest(hermes_env):
+    hermes_env['hermes.toml'] = ""
+
     with hermes_env:
         result = hermes_env.run("harvest")
 
     assert result.returncode == 0
 
 
-@pytest.mark.skip(reason="Needs update")
 def test_hermes_process(hermes_env):
+    hermes_env['hermes.toml'] = ""
+    hermes_env['.hermes/harvest/test.json'] = ""
+
     with hermes_env:
         result = hermes_env.run("process")
+        print(result.stdout.read())
 
     assert result.returncode == 0

From 7f64f102e916c76dc44404b77ab2a80f5a4e59b1 Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 6 Aug 2024 14:41:28 +0200
Subject: [PATCH 04/20] Add basic error handling to console entry point

---
 src/hermes/commands/cli.py | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/src/hermes/commands/cli.py b/src/hermes/commands/cli.py
index 5ca827de..dae31858 100644
--- a/src/hermes/commands/cli.py
+++ b/src/hermes/commands/cli.py
@@ -9,6 +9,7 @@
 This module provides the main entry point for the HERMES command line application.
 """
 import argparse
+import sys
 
 from hermes import logger
 from hermes.commands import HermesHelpCommand, HermesCleanCommand, HermesHarvestCommand, HermesProcessCommand, \
@@ -58,7 +59,22 @@ def main() -> None:
     args = parser.parse_args()
 
     logger.init_logging()
+    log = logger.getLogger("hermes.cli")
+    log.debug("Running hermes with the following command line arguments: %s", args)
 
-    args.command.load_settings(args)
-    args.command.patch_settings(args)
-    args.command(args)
+    try:
+        log.info("Loading settings...")
+        args.command.load_settings(args)
+
+        log.debug("Update settings from command line...")
+        args.command.patch_settings(args)
+
+        log.info("Run subcommand %s", args.command.command_name)
+        args.command(args)
+    except BaseException as e:
+        log.error("An error occurred during execution of %s", args.command.command_name)
+        log.debug("Original exception was: %s", e)
+
+        sys.exit(1)
+
+    sys.exit(0)

From c27192c055853a321f1d64d20748ba267f80bd3c Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 6 Aug 2024 14:59:10 +0200
Subject: [PATCH 05/20] Adapt commands and plugins to propagate errors

There is no consistent use yet, some exceptions are re-raised, some are logged to an internal error register of the command...
---
 src/hermes/commands/base.py                    | 1 +
 src/hermes/commands/cli.py                     | 7 ++++++-
 src/hermes/commands/deposit/base.py            | 4 +++-
 src/hermes/commands/deposit/invenio.py         | 2 +-
 src/hermes/commands/harvest/base.py            | 4 +++-
 src/hermes/commands/postprocess/invenio.py     | 4 ++--
 src/hermes/commands/postprocess/invenio_rdm.py | 4 ++--
 src/hermes/commands/process/base.py            | 3 ++-
 8 files changed, 20 insertions(+), 9 deletions(-)

diff --git a/src/hermes/commands/base.py b/src/hermes/commands/base.py
index dea22412..82692975 100644
--- a/src/hermes/commands/base.py
+++ b/src/hermes/commands/base.py
@@ -43,6 +43,7 @@ def __init__(self, parser: argparse.ArgumentParser):
         self.settings = None
 
         self.log = logging.getLogger(f"hermes.{self.command_name}")
+        self.errors = []
 
     def init_plugins(self):
         """Collect and initialize the plugins available for the HERMES command."""
diff --git a/src/hermes/commands/cli.py b/src/hermes/commands/cli.py
index dae31858..167d1beb 100644
--- a/src/hermes/commands/cli.py
+++ b/src/hermes/commands/cli.py
@@ -71,10 +71,15 @@ def main() -> None:
 
         log.info("Run subcommand %s", args.command.command_name)
         args.command(args)
-    except BaseException as e:
+    except Exception as e:
         log.error("An error occurred during execution of %s", args.command.command_name)
         log.debug("Original exception was: %s", e)
 
+        sys.exit(2)
+
+    if args.command.errors:
+        for e in args.command.errors:
+            log.error(e)
         sys.exit(1)
 
     sys.exit(0)
diff --git a/src/hermes/commands/deposit/base.py b/src/hermes/commands/deposit/base.py
index 5f0290c2..0a8e10f5 100644
--- a/src/hermes/commands/deposit/base.py
+++ b/src/hermes/commands/deposit/base.py
@@ -134,11 +134,13 @@ def __call__(self, args: argparse.Namespace) -> None:
         try:
             plugin_func = self.plugins[plugin_name](self, ctx)
 
-        except KeyError:
+        except KeyError as e:
             self.log.error("Plugin '%s' not found.", plugin_name)
+            self.errors.append(e)
 
         try:
             plugin_func(self)
 
         except HermesValidationError as e:
             self.log.error("Error while executing %s: %s", plugin_name, e)
+            self.errors.append(e)
diff --git a/src/hermes/commands/deposit/invenio.py b/src/hermes/commands/deposit/invenio.py
index 6c8ff139..ddee7e68 100644
--- a/src/hermes/commands/deposit/invenio.py
+++ b/src/hermes/commands/deposit/invenio.py
@@ -105,7 +105,7 @@ class InvenioResolver:
     invenio_client_class = InvenioClient
 
     def __init__(self, client=None):
-        self.client = client or self.invenio_client_class()
+        self.client = client or self.invenio_client_class(InvenioDepositSettings())
 
     def resolve_latest_id(
         self, record_id=None, doi=None, codemeta_identifier=None
diff --git a/src/hermes/commands/harvest/base.py b/src/hermes/commands/harvest/base.py
index 629342e7..4d2a1731 100644
--- a/src/hermes/commands/harvest/base.py
+++ b/src/hermes/commands/harvest/base.py
@@ -57,8 +57,10 @@ def __call__(self, args: argparse.Namespace) -> None:
                         if any(v != _value and t == _tag for v, t in _trace):
                             raise MergeError(_key, None, _value)
 
-            except KeyError:
+            except KeyError as e:
                 self.log.error("Plugin '%s' not found.", plugin_name)
+                self.errors.append(e)
 
             except HermesValidationError as e:
                 self.log.error("Error while executing %s: %s", plugin_name, e)
+                self.errors.append(e)
diff --git a/src/hermes/commands/postprocess/invenio.py b/src/hermes/commands/postprocess/invenio.py
index 7d039ae1..bf3a7df3 100644
--- a/src/hermes/commands/postprocess/invenio.py
+++ b/src/hermes/commands/postprocess/invenio.py
@@ -23,8 +23,8 @@ def config_record_id(ctx):
     try:
         conf.deposit.invenio.record_id = deposition['record_id']
         toml.dump(conf, open('hermes.toml', 'w'))
-    except KeyError:
-        raise RuntimeError("No deposit.invenio configuration available to store record id in") from None
+    except KeyError as e:
+        raise RuntimeError("No deposit.invenio configuration available to store record id in") from e
 
 
 def cff_doi(ctx):
diff --git a/src/hermes/commands/postprocess/invenio_rdm.py b/src/hermes/commands/postprocess/invenio_rdm.py
index 7b2bf37c..ddbc8cb4 100644
--- a/src/hermes/commands/postprocess/invenio_rdm.py
+++ b/src/hermes/commands/postprocess/invenio_rdm.py
@@ -22,5 +22,5 @@ def config_record_id(ctx):
     try:
         conf['deposit']['invenio_rdm']['record_id'] = deposition['record_id']
         toml.dump(conf, open('hermes.toml', 'w'))
-    except KeyError:
-        raise RuntimeError("No deposit.invenio configuration available to store record id in") from None
+    except KeyError as e:
+        raise RuntimeError("No deposit.invenio configuration available to store record id in") from e
diff --git a/src/hermes/commands/process/base.py b/src/hermes/commands/process/base.py
index 8abeacc5..9e29d1e6 100644
--- a/src/hermes/commands/process/base.py
+++ b/src/hermes/commands/process/base.py
@@ -58,7 +58,8 @@ def __call__(self, args: argparse.Namespace) -> None:
             ctx.merge_contexts_from(harvest_context)
 
         if ctx._errors:
-            self.log.error('!!! warning "Errors during merge"')
+            self.log.error('Errors during merge')
+            self.errors.extend(ctx._errors)
 
             for ep, error in ctx._errors:
                 self.log.info("    - %s: %s", ep.name, error)

From 241f91b1df7605d05f9629188fe6f77cb115df56 Mon Sep 17 00:00:00 2001
From: Michael Meinel <michael.meinel@dlr.de>
Date: Tue, 13 Aug 2024 13:51:32 +0200
Subject: [PATCH 06/20] Apply suggestions from code review

---
 src/hermes/commands/cli.py                     | 2 +-
 src/hermes/commands/postprocess/invenio.py     | 4 ++--
 src/hermes/commands/postprocess/invenio_rdm.py | 4 ++--
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/hermes/commands/cli.py b/src/hermes/commands/cli.py
index 167d1beb..542ff891 100644
--- a/src/hermes/commands/cli.py
+++ b/src/hermes/commands/cli.py
@@ -63,7 +63,7 @@ def main() -> None:
     log.debug("Running hermes with the following command line arguments: %s", args)
 
     try:
-        log.info("Loading settings...")
+        log.debug("Loading settings...")
         args.command.load_settings(args)
 
         log.debug("Update settings from command line...")
diff --git a/src/hermes/commands/postprocess/invenio.py b/src/hermes/commands/postprocess/invenio.py
index bf3a7df3..a7ba6b53 100644
--- a/src/hermes/commands/postprocess/invenio.py
+++ b/src/hermes/commands/postprocess/invenio.py
@@ -23,8 +23,8 @@ def config_record_id(ctx):
     try:
         conf.deposit.invenio.record_id = deposition['record_id']
         toml.dump(conf, open('hermes.toml', 'w'))
-    except KeyError as e:
-        raise RuntimeError("No deposit.invenio configuration available to store record id in") from e
+    except KeyError:
+        raise RuntimeError("No deposit.invenio configuration available to store record id in")
 
 
 def cff_doi(ctx):
diff --git a/src/hermes/commands/postprocess/invenio_rdm.py b/src/hermes/commands/postprocess/invenio_rdm.py
index ddbc8cb4..9553f47b 100644
--- a/src/hermes/commands/postprocess/invenio_rdm.py
+++ b/src/hermes/commands/postprocess/invenio_rdm.py
@@ -22,5 +22,5 @@ def config_record_id(ctx):
     try:
         conf['deposit']['invenio_rdm']['record_id'] = deposition['record_id']
         toml.dump(conf, open('hermes.toml', 'w'))
-    except KeyError as e:
-        raise RuntimeError("No deposit.invenio configuration available to store record id in") from e
+    except KeyError:
+        raise RuntimeError("No deposit.invenio_rdm configuration available to store record id in")

From 7602e3d2647c4f877a525bc36cdb1cd583fd01b4 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 11:22:09 +0200
Subject: [PATCH 07/20] Use template to publish

---
 .github/workflows/hermes-zenodo-sandbox.yml | 146 ++++++++++++++++++--
 1 file changed, 134 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/hermes-zenodo-sandbox.yml b/.github/workflows/hermes-zenodo-sandbox.yml
index 5a036b26..4a6c6aae 100644
--- a/.github/workflows/hermes-zenodo-sandbox.yml
+++ b/.github/workflows/hermes-zenodo-sandbox.yml
@@ -8,24 +8,146 @@ name: Software publication on Zenodo Sandbox
 
 on:
   push:
-    tags:
-      - "*"
+    branches:
+      - feature/261-put-hermes-on-zenodo
+    #tags:
+    #  - "*"
+
+  # NOTE: Do not delete the trigger on closed pull requests, the HERMES workflow needs this.
+  pull_request:
+    types:
+      - closed
 
 jobs:
-  hermes:
-    name: HERMES
+  hermes-prepare:
+    name: Prepare Metadata for Curation
+    runs-on: ubuntu-latest
+    # This condition becomes much easier when we only react to push events on the release branch.
+    # We still need to exclude the merge commit push of the post processing PR
+
+    # ADAPT
+    # Depending on the event you react to in the 'on:' section above, you will need to adapt this
+    # to react on the specific events.
+    # NOTE: You will probably still need to keep the exclusion check for commit messages provided by the workflow ('hermes/'/'hermes/post').
+    if: >
+      github.event_name == 'push' && ! (
+        startsWith(github.ref_name, 'hermes/') ||
+        contains(github.event.head_commit.message, 'hermes/post')
+      )
+
+    permissions:
+      contents: write # Allow creation of new branches
+      pull-requests: write # Postprocessing should be able to create a pull request with changes
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
+        with:
+          python-version: '3.10'
+      - run: pip install hermes
+      - run: hermes harvest
+      - run: hermes process
+      - run: hermes curate
+
+      - run: |
+          # Cache current branch for PR close job
+          git branch --show-current > .hermes/curate/target_branch
+
+          # Shorten the SHA for the PR title
+          SHORT_SHA=$(echo "$GITHUB_SHA" | cut -c -8)
+          echo "SHORT_SHA=$SHORT_SHA" >> "$GITHUB_ENV"
+
+          # Create a curation branch
+          git branch -c "hermes/curate-$SHORT_SHA"
+          git push origin "hermes/curate-$SHORT_SHA"
+
+          # Explicitly add to-be-curated metadata (which is ignored via .gitignore!)
+          git add -f .hermes/curate
+      - uses: peter-evans/create-pull-request@v5
+        with:
+          base: hermes/curate-${{ env.SHORT_SHA }}
+          branch: hermes/curate-result-${{ env.SHORT_SHA }}
+          title: Metadata Curation for Commit ${{ env.SHORT_SHA }}
+          body: |
+            Please carefully review the attached metadata.
+            If you are satisfied with the result, you may merge this PR, which will trigger publication.
+            (Any temporary branches will be cleaned up.)
+          delete-branch: true
+
+  hermes-curate:
+    name: Publish Software with Curated Metadata
+    if: github.event.pull_request.merged == true && startsWith( github.base_ref , 'hermes/curate-')
+
     runs-on: ubuntu-latest
     permissions:
-      contents: read # We will only read content from the repo
-      # pull-requests: write # Postprocessing should be able to create a pull request with changes
+      contents: write # Allow creation of new branches
+      pull-requests: write # Postprocessing should be able to create a pull request with changes
+
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-      - run: pip install git+https://github.com/sdruskat/workflow.git@deRSE23
+      - run: pip install hermes
+
+      # ADAPT
+      # If you want to publish artifacts (e.g., a zipped snapshot of your repository),
+      # you can prepare this here.
       - run: git archive --format zip HEAD src > hermes.zip
-      - run: hermes
-      - run: hermes deposit --auth-token ${{ secrets.ZENODO }} --file hermes.zip --file README.md
-      # - run: hermes postprocess # (Not implemented yet)
-      # - uses: peter-evans/create-pull-request@v4 (TODO once postprocessing has it)
+
+      # Run the HERMES deposition and postprocessing steps.
+      # ADAPT
+      # 1. You need to have an authentication token for your target publication platform
+      #    as a GitHub secret in your repository (in this example, this is called ZENODO_SANDBOX).
+      # 2. Adapt the files you want to deposit. In the example, showcase.zip and README.md are deposited alongside the metadata.
+      # 3. Check if you want to run with '--initial', as this may potentially create a completely new record (collection),
+      #    rather than a new version of the same collection!
+      - run: hermes deposit --initial -O invenio_rdm.auth_token ${{ secrets.ZENODO_SANDBOX }} --file hermes.zip --file README.md
+
+      # ADAPT
+      # Remove this command if you don't want to do any postprocessing
+      - run: hermes postprocess
+
+      # ADAPT
+      # If you don't want to run postprocessing, remove this complete section (next '-run' and 'uses: peter-evans/...' bullets).
+      #
+      # Note 1: We change the base branch here for the PR. This flow runs so far within the "curated-metadata-*" branch,
+      #         but now we want to add the changes done by deposit and post processing to the branch that was initially
+      #         meant to be published using HERMES.
+      # Note 2: The create-pull-request action will NOT inherit the commits we did in the previous job. It will only look at the
+      #         changes within this local workspace we did *now*.
+      - run: echo "TARGET_BRANCH=$(cat .hermes/curate/target_branch)" >> "$GITHUB_ENV"
+      - uses: peter-evans/create-pull-request@v5
+        with:
+          branch: hermes/post-${{ github.run_id }}
+          base: ${{ env.TARGET_BRANCH }}
+          title: Review hermes post-processing results
+          body: |
+            This is an automated pull request created by HERMES post-processing.
+
+            Please carefully review the changes and finally merge them into your
+
+      # Delete all the curation branches
+      - run: |
+          for BRANCH in $(git ls-remote origin 'refs/heads/hermes/curate-*' | cut -f2 | cut -d'/' -f'3-'); do
+            git push origin --delete "$BRANCH"
+          done
+      # TODO: if: failure() --- delete the curation branches when the deposition failed
+
+
+  hermes-cleanup:
+    name: Cleanup aborted curation branches
+    if: github.event.pull_request.merged == false && startsWith( github.base_ref , 'hermes/curate-')
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write # Allow creation of new branches
+      pull-requests: write # Postprocessing should be able to create a pull request with changes
+
+    steps:
+      - uses: actions/checkout@v3
+      # Delete all the curation branches
+      - run: |
+          for BRANCH in $(git ls-remote origin 'refs/heads/hermes/curate-*' | cut -f2 | cut -d'/' -f'3-'); do
+            git push origin --delete "$BRANCH"
+          done

From de92c6cf3609c819142f7db6288873e3f5e995d1 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 12:57:11 +0200
Subject: [PATCH 08/20] Update to newer version

---
 CITATION.cff | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/CITATION.cff b/CITATION.cff
index 54830b3a..6eed50bc 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -14,9 +14,9 @@ title: hermes
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
-version: "proof-of-concept"
+version: 0.8.0b1
 license: "Apache-2.0"
-abstract: "Proof-of-concept implementation of the HERMES workflow."
+abstract: "Tool to automate software publication. Not stable yet."
 type: software
 authors:
   - given-names: Michael
@@ -49,3 +49,8 @@ authors:
     email: d.pape@hzdr.de
     affiliation: Helmholtz-Zentrum Dresden-Rossendorf (HZDR)
     orcid: 'https://orcid.org/0000-0002-3145-9880'
+  - given-names: Kernchen
+    family-names: Sophie
+    email: sophie.kernchen@dlr.de
+    affiliation: German Aerospace Center (DLR)
+    orcid: 'https://orcid.org/0009-0005-4430-6743'

From 44899564733ecaac592102055d10386ee8c35791 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 13:04:45 +0200
Subject: [PATCH 09/20] Correct variable name

---
 .github/workflows/hermes-zenodo-sandbox.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/hermes-zenodo-sandbox.yml b/.github/workflows/hermes-zenodo-sandbox.yml
index 4a6c6aae..a815df40 100644
--- a/.github/workflows/hermes-zenodo-sandbox.yml
+++ b/.github/workflows/hermes-zenodo-sandbox.yml
@@ -102,7 +102,7 @@ jobs:
       # 2. Adapt the files you want to deposit. In the example, showcase.zip and README.md are deposited alongside the metadata.
       # 3. Check if you want to run with '--initial', as this may potentially create a completely new record (collection),
       #    rather than a new version of the same collection!
-      - run: hermes deposit --initial -O invenio_rdm.auth_token ${{ secrets.ZENODO_SANDBOX }} --file hermes.zip --file README.md
+      - run: hermes deposit --initial -O invenio_rdm.auth_token ${{ secrets.ZENODO }} --file hermes.zip --file README.md
 
       # ADAPT
       # Remove this command if you don't want to do any postprocessing

From 133f8b78f6317b71edd3db888103fb6e168283ca Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 13:13:31 +0200
Subject: [PATCH 10/20] Correct version

---
 CITATION.cff | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CITATION.cff b/CITATION.cff
index 6eed50bc..eea43ed5 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -14,7 +14,7 @@ title: hermes
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
-version: 0.8.0b1
+version: 0.8.1b1
 license: "Apache-2.0"
 abstract: "Tool to automate software publication. Not stable yet."
 type: software

From 1b3b140d99d8278f15bb3f4dfb2ce9676373ded6 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 13:22:55 +0200
Subject: [PATCH 11/20] Push on Zenodo not sandbox

---
 .../{hermes-zenodo-sandbox.yml => hermes-zenodo.yml}        | 6 ++----
 hermes.toml                                                 | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)
 rename .github/workflows/{hermes-zenodo-sandbox.yml => hermes-zenodo.yml} (98%)

diff --git a/.github/workflows/hermes-zenodo-sandbox.yml b/.github/workflows/hermes-zenodo.yml
similarity index 98%
rename from .github/workflows/hermes-zenodo-sandbox.yml
rename to .github/workflows/hermes-zenodo.yml
index a815df40..2db5ae99 100644
--- a/.github/workflows/hermes-zenodo-sandbox.yml
+++ b/.github/workflows/hermes-zenodo.yml
@@ -8,10 +8,8 @@ name: Software publication on Zenodo Sandbox
 
 on:
   push:
-    branches:
-      - feature/261-put-hermes-on-zenodo
-    #tags:
-    #  - "*"
+    tags:
+      - "*"
 
   # NOTE: Do not delete the trigger on closed pull requests, the HERMES workflow needs this.
   pull_request:
diff --git a/hermes.toml b/hermes.toml
index 8884aea4..e2ea3690 100644
--- a/hermes.toml
+++ b/hermes.toml
@@ -12,7 +12,7 @@ enable_validation = false
 target = "invenio_rdm"
 
 [deposit.invenio_rdm]
-site_url = "https://sandbox.zenodo.org"
+site_url = "https://zenodo.org"
 communities = []
 access_right = "open"
 

From 9f8ef98e76773ec3647509e78d8e96c0b1bb7010 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 13:24:51 +0200
Subject: [PATCH 12/20] Change name

---
 .github/workflows/hermes-zenodo.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/hermes-zenodo.yml b/.github/workflows/hermes-zenodo.yml
index 2db5ae99..46cf0390 100644
--- a/.github/workflows/hermes-zenodo.yml
+++ b/.github/workflows/hermes-zenodo.yml
@@ -4,7 +4,7 @@
 
 # SPDX-FileContributor: Stephan Druskat
 
-name: Software publication on Zenodo Sandbox
+name: Software publication on Zenodo
 
 on:
   push:

From 4f27bdd3f6b0829c2dc58ec5e92265fc750d47b5 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 14:02:43 +0200
Subject: [PATCH 13/20] Adapt for release tag not branch

---
 .github/workflows/hermes-zenodo.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/hermes-zenodo.yml b/.github/workflows/hermes-zenodo.yml
index 46cf0390..402c5944 100644
--- a/.github/workflows/hermes-zenodo.yml
+++ b/.github/workflows/hermes-zenodo.yml
@@ -56,7 +56,7 @@ jobs:
           echo "SHORT_SHA=$SHORT_SHA" >> "$GITHUB_ENV"
 
           # Create a curation branch
-          git branch -c "hermes/curate-$SHORT_SHA"
+          git switch -c "hermes/curate-$SHORT_SHA"
           git push origin "hermes/curate-$SHORT_SHA"
 
           # Explicitly add to-be-curated metadata (which is ignored via .gitignore!)

From ad75da370a5d222b452b236b24ad9314367b5010 Mon Sep 17 00:00:00 2001
From: "Kernchen, Sophie" <sophie.kernchen@dlr.de>
Date: Mon, 5 Aug 2024 14:17:38 +0200
Subject: [PATCH 14/20] Add record id and DOI

---
 CITATION.cff | 4 ++++
 hermes.toml  | 1 +
 2 files changed, 5 insertions(+)

diff --git a/CITATION.cff b/CITATION.cff
index eea43ed5..36db497f 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -54,3 +54,7 @@ authors:
     email: sophie.kernchen@dlr.de
     affiliation: German Aerospace Center (DLR)
     orcid: 'https://orcid.org/0009-0005-4430-6743'
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.13221384
+    description: Version 0.8.1b1
diff --git a/hermes.toml b/hermes.toml
index e2ea3690..f455746a 100644
--- a/hermes.toml
+++ b/hermes.toml
@@ -15,6 +15,7 @@ target = "invenio_rdm"
 site_url = "https://zenodo.org"
 communities = []
 access_right = "open"
+record_id = 13221384
 
 [deposit.invenio_rdm.api_paths]
 depositions = "api/deposit/depositions"

From 1c85dec4e681c63f242d6f3d0bd3243e4a0ec64b Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 6 Aug 2024 15:09:31 +0200
Subject: [PATCH 15/20] Bump version of hermes

---
 hermes.toml    | 3 ---
 pyproject.toml | 2 +-
 2 files changed, 1 insertion(+), 4 deletions(-)

diff --git a/hermes.toml b/hermes.toml
index f455746a..fd743ce4 100644
--- a/hermes.toml
+++ b/hermes.toml
@@ -5,9 +5,6 @@
 [harvest]
 sources = [ "cff" ] # ordered priority (first one is most important)
 
-[harvest.cff]
-enable_validation = false
-
 [deposit]
 target = "invenio_rdm"
 
diff --git a/pyproject.toml b/pyproject.toml
index 41bad489..8dd98b12 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -9,7 +9,7 @@
 [tool.poetry]
 # Reference at https://python-poetry.org/docs/pyproject/
 name = "hermes"
-version = "0.1.0"
+version = "0.8.1"
 description = "Workflow to publish research software with rich metadata"
 homepage = "https://software-metadata.pub"
 license = "Apache-2.0"

From a3164e9565b643571ff5c6122defe640ec8ee6ce Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 6 Aug 2024 15:11:38 +0200
Subject: [PATCH 16/20] Remove old settings handler

---
 src/hermes/settings.py | 44 ------------------------------------------
 1 file changed, 44 deletions(-)
 delete mode 100644 src/hermes/settings.py

diff --git a/src/hermes/settings.py b/src/hermes/settings.py
deleted file mode 100644
index fbae7b92..00000000
--- a/src/hermes/settings.py
+++ /dev/null
@@ -1,44 +0,0 @@
-# SPDX-FileCopyrightText: 2024 German Aerospace Center (DLR)
-#
-# SPDX-License-Identifier: Apache-2.0
-
-# SPDX-FileContributor: Sophie Kernchen
-# SPDX-FileContributor: Michael Meinel
-
-import pathlib
-from typing import Any, Dict, Tuple
-
-import toml
-from pydantic.fields import FieldInfo
-from pydantic_settings import PydanticBaseSettingsSource
-
-
-class TomlConfigSettingsSource(PydanticBaseSettingsSource):
-    """
-    A simple settings source class that loads variables from a TOML file
-    at the project's root.
-
-    Here we happen to choose to use the `env_file_encoding` from Config
-    when reading `config.json`
-    """
-    def __init__(self, settings_cls, config_path):
-        super().__init__(settings_cls)
-        self.__config_path = config_path
-
-    def get_field_value(self, field: FieldInfo, field_name: str) -> Tuple[Any, str, bool]:
-        file_content_toml = toml.load(pathlib.Path(self.__config_path))
-        field_value = file_content_toml.get(field_name)
-        return field_value, field_name, False
-
-    def prepare_field_value(self, field_name: str, field: FieldInfo, value: Any, value_is_complex: bool) -> Any:
-        return value
-
-    def __call__(self) -> Dict[str, Any]:
-        d: Dict[str, Any] = {}
-        for field_name, field in self.settings_cls.model_fields.items():
-            field_value, field_key, value_is_complex = self.get_field_value(field, field_name)
-            field_value = self.prepare_field_value(field_name, field, field_value, value_is_complex)
-            if field_value is not None:
-                d[field_key] = field_value
-
-        return d

From 9e40d7e46d23ed7b21eeb13809677a645d66f14d Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 6 Aug 2024 15:12:04 +0200
Subject: [PATCH 17/20] Add missing author to Python package info

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index 8dd98b12..42a4747b 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -20,6 +20,7 @@ authors = [
     "Jeffrey Kelling <j.kelling@hzdr.de>",
     "Oliver Knodel <o.knodel@hzdr.de>",
     "David Pape <d.pape@hzdr.de>",
+    "Sophie Kernchen <sohpie.kernchen@dlr.de>",
 ]
 
 readme = "README.md"

From a418fec5d97cbf19c363c04dc4e960bc74161aae Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 13 Aug 2024 13:54:40 +0200
Subject: [PATCH 18/20] Add log output to ignored files

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index d7c36ebe..5856425f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -23,3 +23,4 @@ dist/
 
 # HERMES workflow specifics
 .hermes/
+hermes.log

From 797b0ca3678aa28c810a32600e35d3021094d8ca Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 13 Aug 2024 13:57:06 +0200
Subject: [PATCH 19/20] Enable harvesting from pyproject.toml

---
 .github/workflows/hermes-zenodo.yml | 2 +-
 hermes.toml                         | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/hermes-zenodo.yml b/.github/workflows/hermes-zenodo.yml
index 402c5944..302fdeb0 100644
--- a/.github/workflows/hermes-zenodo.yml
+++ b/.github/workflows/hermes-zenodo.yml
@@ -42,7 +42,7 @@ jobs:
       - uses: actions/setup-python@v4
         with:
           python-version: '3.10'
-      - run: pip install hermes
+      - run: pip install hermes hermes-plugin-python
       - run: hermes harvest
       - run: hermes process
       - run: hermes curate
diff --git a/hermes.toml b/hermes.toml
index fd743ce4..3aa44a8f 100644
--- a/hermes.toml
+++ b/hermes.toml
@@ -3,7 +3,7 @@
 # SPDX-License-Identifier: CC0-1.0
 
 [harvest]
-sources = [ "cff" ] # ordered priority (first one is most important)
+sources = [ "cff", "toml" ] # ordered priority (first one is most important)
 
 [deposit]
 target = "invenio_rdm"

From 92a1da57cba3935d45650176378e5680463d5b3d Mon Sep 17 00:00:00 2001
From: "Meinel, Michael" <michael.meinel@dlr.de>
Date: Tue, 13 Aug 2024 13:57:38 +0200
Subject: [PATCH 20/20] Bump version number

---
 CITATION.cff | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CITATION.cff b/CITATION.cff
index 36db497f..dfb7efe6 100644
--- a/CITATION.cff
+++ b/CITATION.cff
@@ -14,7 +14,7 @@ title: hermes
 message: >-
   If you use this software, please cite it using the
   metadata from this file.
-version: 0.8.1b1
+version: 0.8.1
 license: "Apache-2.0"
 abstract: "Tool to automate software publication. Not stable yet."
 type: software