Always return cifcheck-errors.

validation/Dockerfile

@@ -7,7 +7,7 @@ ARG VERSION_PYTHON
 ARG VERSION_BASE_IMAGE
 
 ARG VERSION_CPP_DICT_PACK="v2.500"
-ARG VERSION_PY_MMCIF="0.76"
+ARG VERSION_PY_MMCIF="0.79"
 
 ## Set up environment
 ENV MMCIF_DICTS_DIR="/usr/local/share/mmcif-dict-suite" \
@@ -97,7 +97,7 @@ RUN set -e pipefail; \
     gunzip *.gz; \
     #
     ## Fetch the merged ModelCIF dictionary
-    if test x${USE_DICT_VERSION} == xlatest; then \
+    if test x${USE_DICT_VERSION} = xlatest; then \
       export _MA_DICT_URL="${_GIT_URL}/dist/mmcif_ma.dic"; \
     fi; \
     curl ${_MA_DICT_URL} -s -L -o mmcif_ma.dic; \

validation/README.md

-[[_TOC_]]
-
 # ModelCIF validation tool
 
-This is a tool to check that the formatting of ModelCIF files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option [`--extend-validated-file`](#add-validation-dictionary-to-ModelCIF-file)). For more basic mmCIF validation, the dictionary of the underlying PDBx/mmCIF format is also available.
+This is a tool to check that the formatting of [ModelCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Index/) files complies with the ModelCIF format declaration (aka "dictionary"). Upon successful validation, a ModelCIF file can be extended with the dictionary version the file was compared to (option [`--extend-validated-file`](#add-dictionary-information-used-for-validation-to-modelcIF-file)). For more basic [mmCIF](https://mmcif.wwpdb.org) validation, the dictionary of the underlying [PDBx/mmCIF](https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) format is also available.
 
-The easiest way to run validation is from Docker container.
+The easiest way to run validation is from [Docker](https://www.docker.com) container.
 
 The tool itself is a wrapper around the [`CifCheck`](https://github.com/rcsb/cpp-dict-pack) tool by [RCSB](https://www.rcsb.org/).
 
+[[_TOC_]]
+
 
 ## How to run the validation tool
 
-This is just a description of the validation tool itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation container in "[How to run the container](#how-to-run-the-container)".
+This is just a description of the [validation tool](./validate-mmcif-file.py) itself. When running it from inside a container, the command needs to be prefixed with the instructions to start the container. Find information for running the validation Docker container in "[How to run the container](#how-to-run-the-container)".
 
-Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in JSON format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
+Upon completion, if there hasn't been any error running the command, the validation tool returns a concise report in [JSON](https://www.json.org/json-en.html) format. That output is meant to be input to a website or any kind of nicely formatted report. Output can also be stored as a JSON formatted file. If the tested ModelCIF file is fully compliant with the ModelCIF format, the JSON output has
 
 - `status` "completed"
 - no messages in the `diagnosis` list

validation/validate-mmcif-file.py

@@ -476,6 +476,7 @@ class _CifCheck:
         """Run CifCheck for a given file and catch the output.
 
         Returns False if the CifCheck execution itself failed."""
+        self.check_results["cifcheck-errors"] = []
         try:
             format_errors = self._execute(cif_file)
         except _CifCheckFailedError as exc: