Bunch of small refactorings and updates

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 ---
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.1.0
+    rev: v3.4.0
     hooks:
       - id: check-yaml
         files: .*\.(yaml|yml)$
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.23.0
+    rev: v1.26.1
     hooks:
       - id: yamllint
         args: ['-d {extends: relaxed, rules: {line-length: disable}}', '-s']
@@ -17,10 +17,10 @@ repos:
       - id: bashate
         args: ['--ignore=E006']
   - repo: https://gitlab.com/pycqa/flake8
-    rev: 3.8.3
+    rev: 3.9.1
     hooks:
       - id: flake8
   - repo: https://github.com/pre-commit/mirrors-autopep8
-    rev: v1.5.4
+    rev: v1.5.6
     hooks:
       - id: autopep8

.readthedocs.yml

@@ -12,6 +12,6 @@ sphinx:
 formats: all
 
 python:
-  version: 3.7
+  version: 3.8
   install:
     - requirements: requirements-dev.txt

Makefile

@@ -152,6 +152,8 @@ pull/%: DARGS?=
 pull/%: ## pull a jupyter image
 	docker pull $(DARGS) $(OWNER)/$(notdir $@)
 
+pull-all: $(foreach I,$(ALL_IMAGES),pull/$(I) ) ## pull all images
+
 push/%: DARGS?=
 push/%: ## push all tags for a jupyter image
 	docker push --all-tags $(DARGS) $(OWNER)/$(notdir $@)

test/helpers.py

@@ -75,7 +75,7 @@ class CondaPackageHelper:
         if self.specs is None:
             LOGGER.info("Grabing the list of specifications ...")
             self.specs = CondaPackageHelper._packages_from_json(
-                self._execute_command(CondaPackageHelper._conda_export_command(True))
+                self._execute_command(CondaPackageHelper._conda_export_command(from_history=True))
             )
         return self.specs
 
@@ -130,7 +130,7 @@ class CondaPackageHelper:
         return ddict
 
     def check_updatable_packages(self, specifications_only=True):
-        """Check the updatables packages including or not dependencies"""
+        """Check the updatable packages including or not dependencies"""
         specs = self.specified_packages()
         installed = self.installed_packages()
         available = self.available_packages()
@@ -145,9 +145,10 @@ class CondaPackageHelper:
                 current = min(inst_vs, key=CondaPackageHelper.semantic_cmp)
                 newest = avail_vs[-1]
                 if avail_vs and current != newest:
-                    if CondaPackageHelper.semantic_cmp(
+                    if (
-                        current
+                        CondaPackageHelper.semantic_cmp(current) <
-                    ) < CondaPackageHelper.semantic_cmp(newest):
+                        CondaPackageHelper.semantic_cmp(newest)
+                    ):
                         self.comparison.append(
                             {"Package": pkg, "Current": current, "Newest": newest}
                         )
@@ -180,10 +181,7 @@ class CondaPackageHelper:
 
     def get_outdated_summary(self, specifications_only=True):
         """Return a summary of outdated packages"""
-        if specifications_only:
+        nb_packages = len(self.specs if specifications_only else self.installed)
-            nb_packages = len(self.specs)
-        else:
-            nb_packages = len(self.installed)
         nb_updatable = len(self.comparison)
         updatable_ratio = nb_updatable / nb_packages
         return f"{nb_updatable}/{nb_packages} ({updatable_ratio:.0%}) packages could be updated"

test/test_packages.py

@@ -7,12 +7,12 @@ test_packages
 This test module tests if R and Python packages installed can be imported.
 It's a basic test aiming to prove that the package is working properly.
 
-The goal is to detect import errors that can be caused by incompatibilities between packages for example:
+The goal is to detect import errors that can be caused by incompatibilities between packages, for example:
 
 - #1012: issue importing `sympy`
 - #966: isssue importing `pyarrow`
 
-This module checks dynmamically, through the `CondaPackageHelper`, only the specified packages i.e. packages requested by `conda install` in the `Dockerfiles`.
+This module checks dynamically, through the `CondaPackageHelper`, only the specified packages i.e. packages requested by `conda install` in the `Dockerfile`s.
 This means that it does not check dependencies. This choice is a tradeoff to cover the main requirements while achieving reasonable test duration.
 However it could be easily changed (or completed) to cover also dependencies `package_helper.installed_packages()` instead of `package_helper.specified_packages()`.
 
@@ -86,10 +86,7 @@ def packages(package_helper):
 
 def package_map(package):
     """Perform a mapping between the python package name and the name used for the import"""
-    _package = package
+    return PACKAGE_MAPPING.get(package, package)
-    if _package in PACKAGE_MAPPING:
-        _package = PACKAGE_MAPPING.get(_package)
-    return _package
 
 
 def excluded_package_predicate(package):
@@ -136,9 +133,8 @@ def _import_packages(package_helper, filtered_packages, check_function, max_fail
     for package in filtered_packages:
         LOGGER.info(f"Trying to import {package}")
         try:
-            assert (
+            assert check_function(package_helper, package) == 0, \
-                check_function(package_helper, package) == 0
+                f"Package [{package}] import failed"
-            ), f"Package [{package}] import failed"
         except AssertionError as err:
             failures[package] = err
     if len(failures) > max_failures: