From 844eeab02b26ed4b1af640c31581c355dcee0037 Mon Sep 17 00:00:00 2001 From: Alex Nelson Date: Wed, 10 Nov 2021 09:34:40 -0500 Subject: [PATCH 1/5] Bump CASE-Examples-QC pointer --- dependencies/CASE-Examples-QC | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dependencies/CASE-Examples-QC b/dependencies/CASE-Examples-QC index 49e1bdf..6ccbb32 160000 --- a/dependencies/CASE-Examples-QC +++ b/dependencies/CASE-Examples-QC @@ -1 +1 @@ -Subproject commit 49e1bdf7d6f366dc18655ace5ea3043e84493767 +Subproject commit 6ccbb32b3bb195e5e2fed7d8dafc89a0e3e8b652 From 12b26b8badbcab1ea807c0ba58f8e59e56bc7450 Mon Sep 17 00:00:00 2001 From: Alex Nelson Date: Wed, 10 Nov 2021 09:35:01 -0500 Subject: [PATCH 2/5] Clean whitespace --- tests/Makefile | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/Makefile b/tests/Makefile index 340aca2..9ceb8d6 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -52,7 +52,6 @@ all: \ . touch $@ - all-case_utils: \ .venv.done.log $(MAKE) \ From d360c7b1823879ce55859ba45e982cad8402668c Mon Sep 17 00:00:00 2001 From: Alex Nelson Date: Wed, 10 Nov 2021 09:43:10 -0500 Subject: [PATCH 3/5] Sort imports --- case_utils/case_sparql_select/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/case_utils/case_sparql_select/__init__.py b/case_utils/case_sparql_select/__init__.py index 2580b89..7bbb809 100644 --- a/case_utils/case_sparql_select/__init__.py +++ b/case_utils/case_sparql_select/__init__.py @@ -30,8 +30,8 @@ import argparse import binascii -import os import logging +import os import pandas as pd # type: ignore import rdflib.plugins.sparql # type: ignore From b393a3712f90a0ec1b915fe0ea0e0b6603ce2fee Mon Sep 17 00:00:00 2001 From: Alex Nelson Date: Wed, 10 Nov 2021 09:53:36 -0500 Subject: [PATCH 4/5] Use one rdf-toolkit.jar --- Makefile | 3 ++- tests/case_utils/case_file/Makefile | 4 +++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 5222197..1ec8807 100644 --- a/Makefile +++ b/Makefile @@ -37,7 +37,8 @@ all: \ # Build an ontology terms list, which has a side effect of initiating further submodules. $(MAKE) \ --directory dependencies/CASE-Examples-QC \ - download + .git_submodule_init.done.log \ + .venv.done.log $(MAKE) \ --directory dependencies/CASE-Examples-QC/tests \ ontology_vocabulary.txt diff --git a/tests/case_utils/case_file/Makefile b/tests/case_utils/case_file/Makefile index f63e264..a771381 100644 --- a/tests/case_utils/case_file/Makefile +++ b/tests/case_utils/case_file/Makefile @@ -17,9 +17,11 @@ top_srcdir := $(shell cd ../../.. ; pwd) tests_srcdir := $(top_srcdir)/tests +case_srcdir := $(top_srcdir)/dependencies/CASE + qc_srcdir := $(top_srcdir)/dependencies/CASE-Examples-QC -RDF_TOOLKIT_JAR := $(qc_srcdir)/dependencies/CASE-Examples/dependencies/CASE-0.3.0/CASE/lib/rdf-toolkit.jar +RDF_TOOLKIT_JAR := $(case_srcdir)/lib/rdf-toolkit.jar COMM ?= $(shell which gcomm 2>/dev/null || which comm) ifeq ($(COMM),) From edeff218a42111ff2617602f16ce4006d4137a47 Mon Sep 17 00:00:00 2001 From: Alex Nelson Date: Wed, 10 Nov 2021 13:12:22 -0500 Subject: [PATCH 5/5] Reduce Python 3 detection With AC-195, macOS environments no longer need to search for other Python 3 deployments that might have `virtualenv`. References: * [AC-195] Use Python venv instead of virtualenv to build virtual environments for CI Signed-off-by: Alex Nelson --- Makefile | 2 +- tests/Makefile | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index 1ec8807..fa526f6 100644 --- a/Makefile +++ b/Makefile @@ -13,7 +13,7 @@ SHELL := /bin/bash -PYTHON3 ?= $(shell which python3.9 2>/dev/null || which python3.8 2>/dev/null || which python3.7 2>/dev/null || which python3.6 2>/dev/null || which python3) +PYTHON3 ?= python3 case_version := $(shell $(PYTHON3) case_utils/ontology/version_info.py) ifeq ($(case_version),) diff --git a/tests/Makefile b/tests/Makefile index 9ceb8d6..25fa731 100644 --- a/tests/Makefile +++ b/tests/Makefile @@ -15,7 +15,7 @@ SHELL := /bin/bash top_srcdir := $(shell cd .. ; pwd) -PYTHON3 ?= $(shell which python3.9 2>/dev/null || which python3.8 2>/dev/null || which python3.7 2>/dev/null || which python3.6 2>/dev/null || which python3) +PYTHON3 ?= python3 all: \ all-case_utils