From 27492e5cc220d0812eb46f08b0859a10d75d0269 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 17:22:52 -0700 Subject: [PATCH 1/8] Use macos 13 --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 3fb312e1..83039554 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -268,7 +268,7 @@ jobs: strategy: matrix: - os: [ubuntu-22.04, windows-2022, macos-12] + os: [ubuntu-22.04, windows-2022, macos-13] r: [4.1.3, 4.2.2, 4.3.1] runs-on: ${{ matrix.os }} From d0d32acbe1f1ba34c20006aedfa61cb81ab417a2 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 19:48:30 -0700 Subject: [PATCH 2/8] Update to use python client 3.1.1 --- DESCRIPTION | 2 +- NEWS.md | 7 +++++++ R/zzz.R | 10 ++++++---- tools/installPythonClient.R | 5 +++-- 4 files changed, 17 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 683211f2..587a7987 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: synapser Type: Package Title: R Language Bindings for Synapse API -Version: 1.2.0 +Version: 1.3.0 Date: 2022-01-18 Authors@R: c( person("Bruce", "Hoff", role = c("aut", "cre"), email = "bruce.hoff@sagebase.org"), diff --git a/NEWS.md b/NEWS.md index 7fce9caa..11abd66d 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,8 +1,15 @@ +## synapser 1.3.0 + +### Improvements + +* Python synapsePythonClient dependency updated to 3.1.1 + ## synapser 1.2.0 ### Improvements * Python synapsePythonClient dependency updated to 3.0.0 +* Use `virtualenv` to install Python dependencies ## synapser 1.1.0 diff --git a/R/zzz.R b/R/zzz.R index ab55d54e..5d5b6695 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -12,10 +12,12 @@ # Ideally we would source tools/installPythonClient.R to not # have to duplicate the synapseclient install code # system2(paste("Rscript ", getwd(), "/tools/installPythonClient.R ", getwd(), sep="")) - PYTHON_CLIENT_VERSION <- '3.0.0' - reticulate::py_install(c("requests", "pandas", "pysftp", "jinja2", "markupsafe")) - reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) - reticulate::py_run_string("import synapseclient") + PYTHON_CLIENT_VERSION <- '3.1.1' + reticulate::virtualenv_create('r-reticulate') + reticulate::use_virtualenv('r-reticulate') + reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) + # reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) + system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') } ) diff --git a/tools/installPythonClient.R b/tools/installPythonClient.R index f206a2e3..3bae45d1 100644 --- a/tools/installPythonClient.R +++ b/tools/installPythonClient.R @@ -5,7 +5,7 @@ # Author: bhoff ############################################################################### -PYTHON_CLIENT_VERSION <- '3.0.0' +PYTHON_CLIENT_VERSION <- '3.1.1' args <- commandArgs(trailingOnly = TRUE) baseDir<-args[1] @@ -19,4 +19,5 @@ reticulate::use_virtualenv('r-reticulate') # reticulate::py_run_string("import sys") # reticulate::py_run_string(sprintf("sys.path.append(\"%s\")", file.path(baseDir, "inst", "python"))) reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) -reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) +#reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) +system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') From ab5d3c8348b205c7a4dfb1592ff2ebf2115205cc Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 19:54:42 -0700 Subject: [PATCH 3/8] Add system call to install --- R/zzz.R | 1 + tools/installPythonClient.R | 1 + 2 files changed, 2 insertions(+) diff --git a/R/zzz.R b/R/zzz.R index 5d5b6695..468c36b7 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -17,6 +17,7 @@ reticulate::use_virtualenv('r-reticulate') reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) # reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) + system('virtualenv r-reticulate') system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') } ) diff --git a/tools/installPythonClient.R b/tools/installPythonClient.R index 3bae45d1..334596b3 100644 --- a/tools/installPythonClient.R +++ b/tools/installPythonClient.R @@ -20,4 +20,5 @@ reticulate::use_virtualenv('r-reticulate') # reticulate::py_run_string(sprintf("sys.path.append(\"%s\")", file.path(baseDir, "inst", "python"))) reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) #reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) +system('virtualenv r-reticulate') system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') From 0f29faa386e4cff0058c9e8a52468b8ca17173d8 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 19:58:58 -0700 Subject: [PATCH 4/8] Update R version --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 83039554..5761c3bd 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -29,7 +29,7 @@ jobs: matrix: # os: [ubuntu-22.04, macos-12, macos-13, windows-2022] os: [ubuntu-22.04, macos-13, windows-2022] - r: [4.1.3, 4.2.3, 4.3.1] + r: [4.1.3, 4.2.3, 4.3.2] steps: - name: checkout From 6fb6e2eae279c0d79a9aa14af8130d644fc8bed1 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 20:09:08 -0700 Subject: [PATCH 5/8] Revert changes, but make versions synonymous --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 5761c3bd..98df9e6f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -29,7 +29,7 @@ jobs: matrix: # os: [ubuntu-22.04, macos-12, macos-13, windows-2022] os: [ubuntu-22.04, macos-13, windows-2022] - r: [4.1.3, 4.2.3, 4.3.2] + r: [4.1.3, 4.2.3, 4.3.1] steps: - name: checkout @@ -269,7 +269,7 @@ jobs: strategy: matrix: os: [ubuntu-22.04, windows-2022, macos-13] - r: [4.1.3, 4.2.2, 4.3.1] + r: [4.1.3, 4.2.3, 4.3.1] runs-on: ${{ matrix.os }} From 9f96fee03533bedc9b2b8d045ee822897d5ff626 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 20:12:51 -0700 Subject: [PATCH 6/8] Remove venv --- R/zzz.R | 1 - tools/installPythonClient.R | 1 - 2 files changed, 2 deletions(-) diff --git a/R/zzz.R b/R/zzz.R index 468c36b7..5d5b6695 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -17,7 +17,6 @@ reticulate::use_virtualenv('r-reticulate') reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) # reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) - system('virtualenv r-reticulate') system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') } ) diff --git a/tools/installPythonClient.R b/tools/installPythonClient.R index 334596b3..3bae45d1 100644 --- a/tools/installPythonClient.R +++ b/tools/installPythonClient.R @@ -20,5 +20,4 @@ reticulate::use_virtualenv('r-reticulate') # reticulate::py_run_string(sprintf("sys.path.append(\"%s\")", file.path(baseDir, "inst", "python"))) reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) #reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) -system('virtualenv r-reticulate') system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') From e33082176688305893c72e0cf769e6a2169fadce Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Tue, 31 Oct 2023 20:22:52 -0700 Subject: [PATCH 7/8] Update to 3.1.0 first --- R/zzz.R | 5 ++--- tools/installPythonClient.R | 5 ++--- 2 files changed, 4 insertions(+), 6 deletions(-) diff --git a/R/zzz.R b/R/zzz.R index 5d5b6695..898b631f 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -12,12 +12,11 @@ # Ideally we would source tools/installPythonClient.R to not # have to duplicate the synapseclient install code # system2(paste("Rscript ", getwd(), "/tools/installPythonClient.R ", getwd(), sep="")) - PYTHON_CLIENT_VERSION <- '3.1.1' + PYTHON_CLIENT_VERSION <- '3.1.0' reticulate::virtualenv_create('r-reticulate') reticulate::use_virtualenv('r-reticulate') reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) - # reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) - system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') + reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) } ) diff --git a/tools/installPythonClient.R b/tools/installPythonClient.R index 3bae45d1..c75d5cbe 100644 --- a/tools/installPythonClient.R +++ b/tools/installPythonClient.R @@ -5,7 +5,7 @@ # Author: bhoff ############################################################################### -PYTHON_CLIENT_VERSION <- '3.1.1' +PYTHON_CLIENT_VERSION <- '3.1.0' args <- commandArgs(trailingOnly = TRUE) baseDir<-args[1] @@ -19,5 +19,4 @@ reticulate::use_virtualenv('r-reticulate') # reticulate::py_run_string("import sys") # reticulate::py_run_string(sprintf("sys.path.append(\"%s\")", file.path(baseDir, "inst", "python"))) reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) -#reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) -system('pip3 install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple "synapseclient[pandas]"') +reticulate::py_install(c(paste("synapseclient==", PYTHON_CLIENT_VERSION, sep="")), pip=T) From 5d19a4320cdec40b02fced1b2f99184bcfaff584 Mon Sep 17 00:00:00 2001 From: Thomas Yu Date: Wed, 1 Nov 2023 15:24:22 -0700 Subject: [PATCH 8/8] Push to version 3.1.1 --- R/zzz.R | 2 +- tools/installPythonClient.R | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/zzz.R b/R/zzz.R index 898b631f..afa9c726 100644 --- a/R/zzz.R +++ b/R/zzz.R @@ -12,7 +12,7 @@ # Ideally we would source tools/installPythonClient.R to not # have to duplicate the synapseclient install code # system2(paste("Rscript ", getwd(), "/tools/installPythonClient.R ", getwd(), sep="")) - PYTHON_CLIENT_VERSION <- '3.1.0' + PYTHON_CLIENT_VERSION <- '3.1.1' reticulate::virtualenv_create('r-reticulate') reticulate::use_virtualenv('r-reticulate') reticulate::py_install(c("requests<3", "pandas~=2.0.0", "pysftp", "jinja2", "markupsafe")) diff --git a/tools/installPythonClient.R b/tools/installPythonClient.R index c75d5cbe..ed6d6e71 100644 --- a/tools/installPythonClient.R +++ b/tools/installPythonClient.R @@ -5,7 +5,7 @@ # Author: bhoff ############################################################################### -PYTHON_CLIENT_VERSION <- '3.1.0' +PYTHON_CLIENT_VERSION <- '3.1.1' args <- commandArgs(trailingOnly = TRUE) baseDir<-args[1]