From 76b9887ba34156349c9ff8f16d5cea4074c07c55 Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Fri, 3 May 2024 11:03:51 -0400 Subject: [PATCH 1/7] add back fabber, update codecov --- .circleci/config.yml | 4 ++-- Dockerfile | 2 +- pyproject.toml | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index bf445fd8d..18a585846 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,10 +1,10 @@ version: 2.1 orbs: - codecov: codecov/codecov@1.0.5 + codecov: codecov/codecov@3.2.4 .dockersetup: &dockersetup docker: - - image: pennlinc/aslprep_build:0.0.7 + - image: pennlinc/aslprep_build:0.0.11 working_directory: /src/aslprep runinstall: &runinstall diff --git a/Dockerfile b/Dockerfile index dadba746e..ba701f667 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM pennlinc/aslprep_build:0.0.7 +FROM pennlinc/aslprep_build:0.0.11 # Install aslprep COPY . /src/aslprep diff --git a/pyproject.toml b/pyproject.toml index ae2bfc8b8..d5be1aa6a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -177,7 +177,7 @@ markers = [ ] [tool.coverage.run] -branch = true +branch = false omit = [ "*/tests/*", "*/__init__.py", From 520e7e8224a51d2cb707efb411fab3829228874a Mon Sep 17 00:00:00 2001 From: Matt Cieslak Date: Fri, 3 May 2024 11:39:42 -0400 Subject: [PATCH 2/7] switch to --citeproc --- aslprep/cli/workflow.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/aslprep/cli/workflow.py b/aslprep/cli/workflow.py index ab39d8e51..873902782 100644 --- a/aslprep/cli/workflow.py +++ b/aslprep/cli/workflow.py @@ -158,8 +158,7 @@ def build_boilerplate(config_file, workflow): "-s", "--bibliography", str(load_data("boilerplate.bib")), - "--filter", - "pandoc-citeproc", + "--citeproc", "--metadata", 'pagetitle="ASLPrep citation boilerplate"', str(citation_files["md"]), From a81cd4798d695991f4c3edcfc7d82d7498eeb19f Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 6 May 2024 10:10:19 -0400 Subject: [PATCH 3/7] Try newer version of codecov orb. --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 18a585846..cbf4f9800 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,6 +1,6 @@ version: 2.1 orbs: - codecov: codecov/codecov@3.2.4 + codecov: codecov/codecov@4.0.1 .dockersetup: &dockersetup docker: From 03f9f6aafa94b83ababa95f88f4d965dee1e6a2d Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Mon, 6 May 2024 12:54:41 -0400 Subject: [PATCH 4/7] Add GPG fix. --- .circleci/config.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.circleci/config.yml b/.circleci/config.yml index cbf4f9800..36e3c5c3e 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -594,6 +594,10 @@ jobs: coverage xml - store_artifacts: path: /src/coverage + - run: + # from https://github.com/codecov/codecov-circleci-orb/issues/157#issue-1692263650 + name: Quick fix for GPG error in Codecov + command: mkdir -p ~/.gnupg - codecov/upload: file: /src/coverage/coverage.xml From 75a05e7e89e774e6760efb3afaacf82107979763 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 7 May 2024 10:23:11 -0400 Subject: [PATCH 5/7] Try bumping orb version. --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 36e3c5c3e..486978049 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,6 +1,6 @@ version: 2.1 orbs: - codecov: codecov/codecov@4.0.1 + codecov: codecov/codecov@4.1.0 .dockersetup: &dockersetup docker: From 4e4877bad53fc0a09b86cecc1af94a92f08440dc Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 7 May 2024 13:36:57 -0400 Subject: [PATCH 6/7] Update .circleci/config.yml --- .circleci/config.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index 486978049..aad6936b2 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -1,6 +1,6 @@ version: 2.1 orbs: - codecov: codecov/codecov@4.1.0 + codecov: codecov/codecov@1.0.5 .dockersetup: &dockersetup docker: From 4cc858d69cb6ee446cf2d7c32b7d3b2d71b9d5b9 Mon Sep 17 00:00:00 2001 From: Taylor Salo Date: Tue, 7 May 2024 16:21:17 -0400 Subject: [PATCH 7/7] Update .circleci/config.yml --- .circleci/config.yml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/.circleci/config.yml b/.circleci/config.yml index aad6936b2..7be8e3c48 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -594,10 +594,6 @@ jobs: coverage xml - store_artifacts: path: /src/coverage - - run: - # from https://github.com/codecov/codecov-circleci-orb/issues/157#issue-1692263650 - name: Quick fix for GPG error in Codecov - command: mkdir -p ~/.gnupg - codecov/upload: file: /src/coverage/coverage.xml