Tools update (#1358)

* Draft tidy of workflows

* Fix: mypy should not ignore missing imports

* Added pydocstyle to checkers

* Added check and format make options

* Fix: mutiple entries in same line setup.py

* Change: black line length to 88

* Fix: make check to only perform checks

* Update: Flake8 ignores style (handled by black/isort)

* Add: pydocstyle, disabled in pre-commit

* Add: Makefile `make pre-commit`

* Fix: Ignores for mypy on untyped modules

* Limit scope of pre-commit steps

* Fix: flake8 no longer concerned about line length

* Add: Flake8 to `make check`

* Fix: reduce scope of black and isort

* Fix: Pydocstyle now uses numpy convention

* Fix: workaround for test imports of `automl_common`

* Fix: `mypy` ignores `automl_common` now

* Fix: Limit scope of `black` and `isort` formatting

* Fix: pre-commit performs no file changes now

* Add: `make pre-commit` to `make help`

* Fix: `make help` docstring for `make pre-commit`

* Fix: isort update sections autosklearn, types

* Fix: warnings by flake8 for line length

* Fix: Types section for isort

* Fix: reenable `flake8` formatting checking

* Update: flake8 to use black's line length of 88

* add: ignore D205 pydocstyle

* Fix: Import order for futures

* Fix: flake8 ignore E203

* Fix: Formatting and fixed long lines

* Del: black/isort checker, checked with pre-commit

* Fix: test dummy prediction error msg

* Add: `coverage` to `pyproject.yaml`

* Add: coverage ignore for `if TYPE_CHECKING`

* Fix: missing coma

* Fix: `toml` dependency for pydoctyle in pre-commit

* Fix: isort src path

* Add: `make test`

* Fix: Add name of module to check coverage of

* Maint: isort and black most recent dev

* Fix: import typo

* Change: format now performs individually on each directory

Author: eddiebergman

.codecov.yml

@@ -1,42 +1,46 @@
 #see https://github.com/codecov/support/wiki/Codecov-Yaml
 codecov:
-  notify:
-    require_ci_to_pass: yes
+  require_ci_to_pass: yes
 
 coverage:
-  precision: 2  # 2 = xx.xx%, 0 = xx%
-  round: nearest # how coverage is rounded: down/up/nearest
-  range: 10...90 # custom range of coverage colors from red -> yellow -> green
+
+  # 2 = xx.xx%, 0 = xx%
+  precision: 2
+
+  # https://docs.codecov.com/docs/commit-status
   status:
-    # https://codecov.readme.io/v1.0/docs/commit-status
+
+    # We want our total main project to always remain above 87% coverage, a
+    # drop of 0.20% is allowed. It should fail if coverage couldn't be uploaded
+    # of the CI fails otherwise
     project:
       default:
-        against: auto
-        target: 70% # specify the target coverage for each commit status
-        threshold: 50% # allow this little decrease on project
-        # https://github.com/codecov/support/wiki/Filtering-Branches
-        # branches: master
+        target: 87%
+        threshold: 0.20%
+        if_not_found: failure
         if_ci_failed: error
-    # https://github.com/codecov/support/wiki/Patch-Status
+
+    # The code changed by a PR should have 90% coverage. This is different from the
+    # overall number shown above.
+    # This encourages small PR's as they are easier to test.
     patch:
       default:
-        against: auto
-        target: 30% # specify the target "X%" coverage to hit
-        threshold: 50% # allow this much decrease on patch
-    changes: false
+        target: 90%
+        if_not_found: failure
+        if_ci_failed: error
 
+# We upload additional information on branching with pytest-cov `--cov-branch`
+# This information can be used by codecov.com to increase analysis of code
 parsers:
   gcov:
     branch_detection:
       conditional: true
       loop: true
+      method: true
       macro: false
-      method: false
-  javascript:
-    enable_partials: false
+
 
 comment:
-  layout: header, diff
+  layout: diff, reach
+  behavior: default
   require_changes: false
-  behavior: default  # update if exists else create new
-  branches: *

.flake8

@@ -1,7 +1,12 @@
 [flake8]
-max-line-length = 100
 show-source = True
-application-import-names = autosklearn
-exclude =
+max-line-length = 88
+extend-exclude =
     venv
+    .venv
     build
+extend-ignore =
+    # No whitespace before ':' in [x : y]
+    E203
+    # No lambdas — too strict
+    E731