Update virtual envs

2020-12-18 14:06:28 -05:00 · 2020-12-18 14:06:28 -05:00 · 079547e60d
parent 41f19ed781
commit 079547e60d
7 changed files with 419 additions and 275 deletions
--- a/.github/workflows/integrate.yaml
+++ b/.github/workflows/integrate.yaml
@ -3,6 +3,8 @@ name: tests
 on:
  push:
    #branches: [ develop ]
+env:
+  RENV_PATHS_ROOT: ~/.local/share/renv

 jobs:
  test-on-latest-ubuntu:
@ -26,7 +28,16 @@ jobs:
          sudo Rscript --vanilla -e 'install.packages("rmarkdown", repos="http://cran.us.r-project.org")'
          conda env create -f environment.yml -n test-environment
          source activate test-environment
-          snakemake -j1 renv_install
-          R -e 'renv::settings$use.cache(FALSE)'
-          snakemake -j1 renv_restore
-          bash tests/scripts/run_tests.sh all test 
+      - name: Cache packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.RENV_PATHS_ROOT }}
+          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
+          restore-keys: |
+            ${{ runner.os }}-renv-
+      - name: Restore packages
+        shell: Rscript {0}
+        run: |
+          if (!requireNamespace("renv", quietly = TRUE)) install.packages("renv")
+          renv::restore()
+      - run : bash tests/scripts/run_tests.sh all test 
--- a/docs/change-log.md
+++ b/docs/change-log.md
@ -1,4 +1,7 @@
 # Change Log
+
+## next release (0.3.0)
+- Update R and Python virtual environments
 ## v0.2.3
 - Fix participant IDS in the example analysis workflow
 ## v0.2.2
--- a/docs/developers/virtual-environments.md
+++ b/docs/developers/virtual-environments.md
@ -1,17 +1,21 @@
 ## Python Virtual Environment

 ### Add new packages
-
 Try to install any new package using `conda install -c CHANNEL PACKAGE_NAME` (you can use `pip` if the package is only available there). Make sure your Python virtual environment is active (`conda activate YOUR_ENV`).

 ### Remove packages
 Uninstall packages using the same manager you used to install them `conda remove PACKAGE_NAME` or `pip uninstall PACKAGE_NAME`

-### Update your conda `environment.yaml`
-
-After installing or removing a package you can use the following command in your terminal to update your `environment.yaml` before publishing your pipeline. Note that we ignore the package version for `libfortran` to keep compatibility with Linux:
+### Updating all packages
+Make sure your Python virtual environment is active (`conda activate YOUR_ENV`), then run
 ```bash
-conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' >  environment.yml
+conda update --all
+```
+
+### Update your conda `environment.yaml`
+After installing or removing a package you can use the following command in your terminal to update your `environment.yaml` before publishing your pipeline. Note that we ignore the package version for `libfortran` and `mkl` to keep compatibility with Linux:
+```bash
+conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' | sed 's/^.*mkl=.*$/  - mkl/' >  environment.yml
 ```

 ## R Virtual Environment
@ -26,6 +30,10 @@ conda env export --no-builds | sed 's/^.*libgfortran.*$/  - libgfortran/' >  env
 2. Run `R` to open an R interactive session
 3. Run `renv::remove("PACKAGE_NAME")`

+### Updating all packages
+1. Open your terminal and navigate to RAPIDS' root folder
+2. Run `R` to open an R interactive session
+3. Run `renv::update()`
 ### Update your R `renv.lock`
 After installing or removing a package you can use the following command in your terminal to update your `renv.lock` before publishing your pipeline.

--- a/docs/index.md
+++ b/docs/index.md
@ -13,6 +13,8 @@ RAPIDS is open source, documented, modular, tested, and reproducible. At the mom

    :fontawesome-solid-play: Ready to start? Go to [Installation](setup/installation/), then to [Configuration](setup/configuration/), and then to [Execution](setup/execution/)

+    :fontawesome-solid-sync-alt: Are you upgrading from RAPIDS [beta](https://rapidspitt.readthedocs.io/en/latest/)? Follow this [guide](migrating-from-old-versions)
+
 ## How does it work?

 RAPIDS is formed by R and Python scripts orchestrated by [Snakemake](https://snakemake.readthedocs.io/en/stable/). We suggest you read Snakemake's docs but in short: every link in the analysis chain is atomic and has files as input and output. Behavioral features are processed per sensor and per participant.
--- a/environment.yml
+++ b/environment.yml
@ -1,102 +1,109 @@
-name: rapids202007
+name: rapids202012
 channels:
-  - anaconda
  - conda-forge
  - defaults
 dependencies:
  - _py-xgboost-mutex=2.0
-  - appdirs=1.4.3
-  - arrow=0.15.2
-  - asn1crypto=1.2.0
-  - astropy=4.0.1.post1
-  - attrs=19.3.0
+  - appdirs=1.4.4
+  - arrow=0.16.0
+  - asn1crypto=1.4.0
+  - astropy=4.2
+  - attrs=20.3.0
  - binaryornot=0.4.4
  - blas=1.0
+  - brotlipy=0.7.0
  - bzip2=1.0.8
-  - ca-certificates=2020.6.20
-  - certifi=2020.6.20
-  - cffi=1.13.1
+  - ca-certificates=2020.12.8
+  - certifi=2020.12.5
+  - cffi=1.14.4
  - chardet=3.0.4
-  - click=7.0
+  - click=7.1.2
  - cookiecutter=1.6.0
-  - cryptography=2.7
+  - cryptography=3.3.1
  - datrie=0.8.2
-  - docutils=0.15.2
-  - future=0.18.1
-  - gitdb2=2.0.6
-  - gitpython=3.0.4
-  - idna=2.8
+  - docutils=0.16
+  - future=0.18.2
+  - gitdb=4.0.5
+  - gitdb2=4.0.2
+  - gitpython=3.1.11
+  - idna=2.10
  - imbalanced-learn=0.6.2
-  - importlib_metadata=0.23
+  - importlib-metadata=2.0.0
+  - importlib_metadata=2.0.0
  - intel-openmp=2019.4
-  - jinja2=2.10.3
+  - jinja2=2.11.2
  - jinja2-time=0.2.0
-  - joblib=0.16.0
-  - jsonschema=3.1.1
+  - joblib=1.0.0
+  - jsonschema=3.2.0
  - libblas=3.8.0
  - libcblas=3.8.0
-  - libcxx=9.0.0
-  - libedit=3.1.20181209
-  - libffi=3.2.1
+  - libcxx=10.0.0
+  - libedit=3.1.20191231
+  - libffi=3.3
  - libgfortran
  - liblapack=3.8.0
  - libxgboost=0.90
-  - lightgbm=2.3.0
+  - lightgbm=3.1.1
  - llvm-openmp=10.0.0
  - markupsafe=1.1.1
-  - mkl=2019.4
+  - mkl
  - mkl-service=2.3.0
-  - mkl_fft=1.0.14
-  - mkl_random=1.1.0
-  - more-itertools=7.2.0
-  - ncurses=6.1
-  - numpy=1.17.2
-  - numpy-base=1.17.2
-  - openssl=1.1.1g
-  - pandas=0.25.2
-  - pbr=5.4.3
-  - pip=19.3.1
-  - plotly=4.2.1
+  - mkl_fft=1.2.0
+  - mkl_random=1.1.1
+  - more-itertools=8.6.0
+  - ncurses=6.2
+  - numpy=1.19.2
+  - numpy-base=1.19.2
+  - openssl=1.1.1i
+  - pandas=1.1.5
+  - pbr=5.5.1
+  - pip=20.3.3
+  - plotly=4.14.1
  - poyo=0.5.0
-  - psutil=5.6.3
+  - psutil=5.7.2
  - py-xgboost=0.90
-  - pycparser=2.19
-  - pyopenssl=19.0.0
+  - pycparser=2.20
+  - pyerfa=1.7.1.1
+  - pyopenssl=20.0.1
  - pysocks=1.7.1
-  - python=3.7.3
-  - python-dateutil=2.8.0
+  - python=3.7.9
+  - python-dateutil=2.8.1
  - python_abi=3.7
-  - pytz=2019.3
-  - pyyaml=5.1.2
+  - pytz=2020.4
+  - pyyaml=5.3.1
  - readline=8.0
-  - requests=2.22.0
+  - requests=2.25.0
  - retrying=1.3.3
-  - scikit-learn=0.22.1
-  - scipy=1.3.1
-  - setuptools=41.6.0
-  - six=1.12.0
-  - smmap2=2.0.5
-  - sqlite=3.30.1
-  - tk=8.6.9
-  - urllib3=1.25.6
-  - wheel=0.33.6
+  - scikit-learn=0.23.2
+  - scipy=1.5.2
+  - setuptools=51.0.0
+  - six=1.15.0
+  - smmap=3.0.4
+  - smmap2=3.0.1
+  - sqlite=3.33.0
+  - threadpoolctl=2.1.0
+  - tk=8.6.10
+  - urllib3=1.25.11
+  - wheel=0.36.2
  - whichcraft=0.6.1
-  - wrapt=1.11.2
+  - wrapt=1.12.1
  - xgboost=0.90
-  - xz=5.2.4
-  - yaml=0.1.7
-  - zipp=0.6.0
+  - xz=5.2.5
+  - yaml=0.2.5
+  - zipp=3.4.0
  - zlib=1.2.11
  - pip:
+    - amply==0.1.4
    - configargparse==0.15.1
    - decorator==4.4.2
    - ipython-genutils==0.2.0
    - jupyter-core==4.6.3
    - nbformat==5.0.7
+    - pulp==2.4
+    - pyparsing==2.4.7
    - pyrsistent==0.15.5
    - ratelimiter==1.2.0.post0
-    - snakemake==5.20.1
+    - snakemake==5.30.2
    - toposort==1.5
    - traitlets==4.3.3
-prefix: /usr/local/Caskroom/miniconda/base/envs/rapids202007
-
+prefix: /usr/local/Caskroom/miniconda/base/envs/rapids202012
--- a/renv.lock
+++ b/renv.lock
@ -11,10 +11,10 @@
  "Packages": {
    "BDgraph": {
      "Package": "BDgraph",
-      "Version": "2.62",
+      "Version": "2.63",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "c2b632b048e00a670495f2804767159f"
+      "Hash": "81946367dff8885e6d87e4e12ffc5f92"
    },
    "BH": {
      "Package": "BH",
@ -39,31 +39,31 @@
    },
    "Formula": {
      "Package": "Formula",
-      "Version": "1.2-3",
+      "Version": "1.2-4",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "0537b6f1f38ea1fd514089192724bb6e"
+      "Hash": "cc8c8c4d61346cde1ca60030ff9c241f"
    },
    "Hmisc": {
      "Package": "Hmisc",
-      "Version": "4.4-0",
+      "Version": "4.4-2",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "1016ef46c7ebf841513624ecb22eebc7"
+      "Hash": "66458e906b2112a8b1639964efd77d7c"
    },
    "KernSmooth": {
      "Package": "KernSmooth",
-      "Version": "2.23-16",
+      "Version": "2.23-18",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "997471f25a7ed6c782f0090ce52cc63a"
+      "Hash": "9e703ad8bf0e99f3691f05da32dfe68b"
    },
    "MASS": {
      "Package": "MASS",
-      "Version": "7.3-51.6",
+      "Version": "7.3-53",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "1dad32ac9dbd8057167b2979fb932ff7"
+      "Hash": "d1bc1c8e9c0ace57ec9ffea01021d45f"
    },
    "Matrix": {
      "Package": "Matrix",
@ -74,10 +74,10 @@
    },
    "R6": {
      "Package": "R6",
-      "Version": "2.4.1",
+      "Version": "2.5.0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "292b54f8f4b94669b08f94e5acce6be2"
+      "Hash": "b203113193e70978a696b2809525649d"
    },
    "RColorBrewer": {
      "Package": "RColorBrewer",
@ -88,31 +88,31 @@
    },
    "RMariaDB": {
      "Package": "RMariaDB",
-      "Version": "1.0.10",
+      "Version": "1.0.11",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "d149479ea03e5cbb1e788449ef5e04b4"
+      "Hash": "0e4f634f2bb38e325717d384a877ccc0"
    },
    "Rcpp": {
      "Package": "Rcpp",
-      "Version": "1.0.4.6",
+      "Version": "1.0.5",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "e652f23d8b1807cc975c51410d05b72f"
+      "Hash": "125dc7a0ed375eb68c0ce533b48d291f"
    },
    "RcppArmadillo": {
      "Package": "RcppArmadillo",
-      "Version": "0.9.870.2.0",
+      "Version": "0.10.1.2.0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "f7fee4557377d47093bd2b65f2642e52"
+      "Hash": "1a885965adade4b8629c478a3b3c2cf7"
    },
    "RcppEigen": {
      "Package": "RcppEigen",
-      "Version": "0.3.3.7.0",
+      "Version": "0.3.3.9.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "c6faf038ba4346b1de19ad7c99b8f94a"
+      "Hash": "ddfa72a87fdf4c80466a20818be91d00"
    },
    "abind": {
      "Package": "abind",
@ -144,10 +144,10 @@
    },
    "backports": {
      "Package": "backports",
-      "Version": "1.1.6",
+      "Version": "1.2.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "3997fd62345a616e59e8161ee0a5816f"
+      "Hash": "644043219fc24e190c2f620c1a380a69"
    },
    "base64enc": {
      "Package": "base64enc",
@ -170,26 +170,40 @@
      "Repository": "CRAN",
      "Hash": "9fe98599ca456d6552421db0d6772d8f"
    },
-    "boot": {
-      "Package": "boot",
-      "Version": "1.3-24",
+    "blob": {
+      "Package": "blob",
+      "Version": "1.2.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "72557d88b5f42f01221dfa436de99301"
+      "Hash": "9addc7e2c5954eca5719928131fed98c"
+    },
+    "boot": {
+      "Package": "boot",
+      "Version": "1.3-25",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "bd51734a754b6c2baf28b2d1ebc11e91"
+    },
+    "brio": {
+      "Package": "brio",
+      "Version": "1.1.0",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "570a24963009b9cce0869a0463c83580"
    },
    "broom": {
      "Package": "broom",
-      "Version": "0.5.6",
+      "Version": "0.7.3",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "754fdb4d17d4ae871343ff2909728ca3"
+      "Hash": "5581a5ddc8fe2ac5e0d092ec2de4c4ae"
    },
    "callr": {
      "Package": "callr",
-      "Version": "3.4.3",
+      "Version": "3.5.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "643163a00cb536454c624883a10ae0bc"
+      "Hash": "b7d7f1e926dfcd57c74ce93f5c048e80"
    },
    "cellranger": {
      "Package": "cellranger",
@ -207,24 +221,24 @@
    },
    "class": {
      "Package": "class",
-      "Version": "7.3-16",
+      "Version": "7.3-17",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "ebc639c4432a2e9c17f195d004848100"
+      "Hash": "9267f5dab59a4ef44229858a142bded1"
    },
    "cli": {
      "Package": "cli",
-      "Version": "2.0.2",
+      "Version": "2.2.0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "ff0becff7bfdfe3f75d29aff8f3172dd"
+      "Hash": "3ef298932294b775fa0a3eeaa3a645b0"
    },
    "clipr": {
      "Package": "clipr",
-      "Version": "0.7.0",
+      "Version": "0.7.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "08cf4045c149a0f0eaf405324c7495bd"
+      "Hash": "ebaa97ac99cc2daf04e77eecc7b781d7"
    },
    "cluster": {
      "Package": "cluster",
@ -235,17 +249,24 @@
    },
    "codetools": {
      "Package": "codetools",
-      "Version": "0.2-16",
+      "Version": "0.2-18",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "89cf4b8207269ccf82fbeb6473fd662b"
+      "Hash": "019388fc48e48b3da0d3a76ff94608a8"
    },
    "colorspace": {
      "Package": "colorspace",
-      "Version": "1.4-1",
+      "Version": "2.0-0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "6b436e95723d1f0e861224dd9b094dfb"
+      "Hash": "abea3384649ef37f60ef51ce002f3547"
+    },
+    "commonmark": {
+      "Package": "commonmark",
+      "Version": "1.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "0f22be39ec1d141fd03683c06f3a6e67"
    },
    "corpcor": {
      "Package": "corpcor",
@ -254,6 +275,13 @@
      "Repository": "CRAN",
      "Hash": "ae01381679f4511ca7a72d55fe175213"
    },
+    "cpp11": {
+      "Package": "cpp11",
+      "Version": "0.2.4",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "ba66e5a750d39067d888aa7af797fed2"
+    },
    "crayon": {
      "Package": "crayon",
      "Version": "1.3.4",
@ -277,17 +305,17 @@
    },
    "data.table": {
      "Package": "data.table",
-      "Version": "1.12.8",
+      "Version": "1.13.4",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "cd711af60c47207a776213a368626369"
+      "Hash": "626afb25b020646f53105e6485e695c6"
    },
    "dbplyr": {
      "Package": "dbplyr",
-      "Version": "1.4.3",
+      "Version": "2.0.0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "81ae261735c247d9551126462db5a4b5"
+      "Hash": "714005206038b1dda74cb1de85029a20"
    },
    "desc": {
      "Package": "desc",
@ -296,26 +324,33 @@
      "Repository": "CRAN",
      "Hash": "6c8fe8fa26a23b79949375d372c7b395"
    },
-    "digest": {
-      "Package": "digest",
-      "Version": "0.6.25",
+    "diffobj": {
+      "Package": "diffobj",
+      "Version": "0.3.2",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "f697db7d92b7028c4b3436e9603fb636"
+      "Hash": "16533929cf545f3c9b796780cccf5eff"
+    },
+    "digest": {
+      "Package": "digest",
+      "Version": "0.6.27",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "a0cbe758a531d054b537d16dff4d58a1"
    },
    "dplyr": {
      "Package": "dplyr",
-      "Version": "0.8.5",
+      "Version": "1.0.2",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "57a42ddf80f429764ff7987128c3fd0a"
+      "Hash": "d0509913b27ea898189ee664b6030dc2"
    },
    "ellipsis": {
      "Package": "ellipsis",
-      "Version": "0.3.0",
+      "Version": "0.3.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "7067d90c1c780bfe80c0d497e3d7b49d"
+      "Hash": "fd2844b3a43ae2d27e70ece2df1b4e2a"
    },
    "entropy": {
      "Package": "entropy",
@ -368,59 +403,59 @@
    },
    "foreach": {
      "Package": "foreach",
-      "Version": "1.5.0",
+      "Version": "1.5.1",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "8fb3ff01ee7d85893f56df8d77213381"
+      "Hash": "e32cfc0973caba11b65b1fa691b4d8c9"
    },
    "foreign": {
      "Package": "foreign",
-      "Version": "0.8-79",
+      "Version": "0.8-80",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "910ad5e5ce9aae0d0f57186ca9a12e1e"
+      "Hash": "ae1b1e15cc6ccb2bc61c0ac33e86d35f"
    },
    "fs": {
      "Package": "fs",
-      "Version": "1.4.1",
+      "Version": "1.5.0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "780713bd2f53156fae001443dcdbdcd5"
+      "Hash": "44594a07a42e5f91fac9f93fda6d0109"
    },
    "generics": {
      "Package": "generics",
-      "Version": "0.0.2",
+      "Version": "0.1.0",
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      "Repository": "CRAN",
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@ -431,24 +466,24 @@
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@ -494,38 +529,38 @@
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@ -536,24 +571,24 @@
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@ -564,31 +599,31 @@
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@ -606,10 +641,10 @@
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@ -620,17 +655,17 @@
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@ -648,17 +683,17 @@
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@ -669,17 +704,17 @@
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@ -739,17 +774,17 @@
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@ -760,10 +795,10 @@
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@ -809,10 +844,10 @@
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@ -823,24 +858,24 @@
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@ -877,12 +912,19 @@
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@ -935,24 +977,24 @@
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@ -970,17 +1012,17 @@
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@ -991,17 +1033,17 @@
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@ -1012,31 +1054,31 @@
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@ -1047,10 +1089,10 @@
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@ -1068,10 +1110,17 @@
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@ -1089,10 +1138,10 @@
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    "viridis": {
      "Package": "viridis",
@ -1108,6 +1157,13 @@
      "Repository": "CRAN",
      "Hash": "ce4f6271baa94776db692f1cb2055bee"
    },
+    "waldo": {
+      "Package": "waldo",
+      "Version": "0.2.3",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Hash": "181d1a31b1ba2009ef20926f2ee0570c"
+    },
    "whisker": {
      "Package": "whisker",
      "Version": "0.4",
@ -1117,17 +1173,17 @@
    },
    "withr": {
      "Package": "withr",
-      "Version": "2.2.0",
+      "Version": "2.3.0",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "ecd17882a0b4419545691e095b74ee89"
+      "Hash": "7307d79f58d1885b38c4f4f1a8cb19dd"
    },
    "xfun": {
      "Package": "xfun",
-      "Version": "0.13",
+      "Version": "0.19",
      "Source": "Repository",
      "Repository": "CRAN",
-      "Hash": "3c1eeacd705ff1695db94bfd443b8a84"
+      "Hash": "a42372606cb76f34da9d090326e9f955"
    },
    "xml2": {
      "Package": "xml2",
--- a/renv/activate.R
+++ b/renv/activate.R
@ -1,10 +1,8 @@

 local({

-  options(tidyverse.quiet = TRUE)
-
  # the requested version of renv
-  version <- "0.10.0"
+  version <- "0.12.3"

  # the project directory
  project <- getwd()
@ -41,8 +39,12 @@ local({
  # load bootstrap tools   
  bootstrap <- function(version, library) {
  
-    # fix up repos
+    # read repos (respecting override if set)
+    repos <- Sys.getenv("RENV_CONFIG_REPOS_OVERRIDE", unset = NA)
+    if (is.na(repos))
      repos <- getOption("repos")
+  
+    # fix up repos
    on.exit(options(repos = repos), add = TRUE)
    repos[repos == "@CRAN@"] <- "https://cloud.r-project.org"
    options(repos = repos)
@ -82,11 +84,19 @@ local({
  
  renv_bootstrap_download <- function(version) {
  
-    methods <- list(
+    # if the renv version number has 4 components, assume it must
+    # be retrieved via github
+    nv <- numeric_version(version)
+    components <- unclass(nv)[[1]]
+  
+    methods <- if (length(components) == 4L) {
+      list(renv_bootstrap_download_github)
+    } else {
+      list(
        renv_bootstrap_download_cran_latest,
-      renv_bootstrap_download_cran_archive,
-      renv_bootstrap_download_github
+        renv_bootstrap_download_cran_archive
      )
+    }
  
    for (method in methods) {
      path <- tryCatch(method(version), error = identity)
@ -100,19 +110,12 @@ local({
  
  renv_bootstrap_download_cran_latest <- function(version) {
  
-    # check for renv on CRAN matching this version
-    db <- as.data.frame(available.packages(), stringsAsFactors = FALSE)
-    if (!"renv" %in% rownames(db))
-      stop("renv is not available on your declared package repositories")
-  
-    entry <- db["renv", ]
-    if (!identical(entry$Version, version))
-      stop("renv is not available on your declared package repositories")
+    repos <- renv_bootstrap_download_cran_latest_find(version)
  
    message("* Downloading renv ", version, " from CRAN ... ", appendLF = FALSE)
  
    info <- tryCatch(
-      download.packages("renv", destdir = tempdir()),
+      download.packages("renv", repos = repos, destdir = tempdir(), quiet = TRUE),
      condition = identity
    )
  
@ -126,6 +129,37 @@ local({
  
  }
  
+  renv_bootstrap_download_cran_latest_find <- function(version) {
+  
+    # check for renv on CRAN matching this version
+    all <- unique(c(
+      getOption("repos"),
+      getOption("renv.bootstrap.repos", default = "https://cloud.r-project.org")
+    ))
+  
+    for (repos in all) {
+  
+      db <- tryCatch(
+        as.data.frame(available.packages(repos = repos), stringsAsFactors = FALSE),
+        error = identity
+      )
+  
+      if (inherits(db, "error"))
+        next
+  
+      entry <- db[db$Package %in% "renv" & db$Version %in% version, ]
+      if (nrow(entry) == 0)
+        next
+  
+      return(repos)
+  
+    }
+  
+    fmt <- "renv %s is not available from your declared package repositories"
+    stop(sprintf(fmt, version))
+  
+  }
+  
  renv_bootstrap_download_cran_archive <- function(version) {
  
    name <- sprintf("renv_%s.tar.gz", version)
@ -259,8 +293,11 @@ local({
      return(path)
  
    path <- Sys.getenv("RENV_PATHS_LIBRARY_ROOT", unset = NA)
-    if (!is.na(path))
-      return(file.path(path, basename(project)))
+    if (!is.na(path)) {
+      id <- substring(renv_bootstrap_hash_text(project), 1L, 8L)
+      name <- paste(basename(project), id, sep = "-")
+      return(file.path(path, name))
+    }
  
    file.path(project, "renv/library")
  
@ -281,8 +318,8 @@ local({
      paste("renv", loadedversion, sep = "@")
  
    fmt <- paste(
-      "renv %1$s was loaded from project library, but renv %2$s is recorded in lockfile.",
-      "Use `renv::record(\"%3$s\")` to record this version in the lockfile.",
+      "renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
+      "Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
      "Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
      sep = "\n"
    )
@ -294,6 +331,16 @@ local({
  
  }
  
+  renv_bootstrap_hash_text <- function(text) {
+  
+    hashfile <- tempfile("renv-hash-")
+    on.exit(unlink(hashfile), add = TRUE)
+  
+    writeLines(text, con = hashfile)
+    tools::md5sum(hashfile)
+  
+  }
+  
  renv_bootstrap_load <- function(project, libpath, version) {
  
    # try to load renv from the project library
@ -304,7 +351,7 @@ local({
    renv_bootstrap_validate_version(version)
  
    # load the project
-    renv::load(project, quiet = TRUE)
+    renv::load(project)
  
    TRUE
  
@ -323,12 +370,22 @@ local({
  if (renv_bootstrap_load(project, libpath, version))
    return(TRUE)

-  # load failed; attempt to bootstrap
+  # load failed; inform user we're about to bootstrap
+  prefix <- paste("# Bootstrapping renv", version)
+  postfix <- paste(rep.int("-", 77L - nchar(prefix)), collapse = "")
+  header <- paste(prefix, postfix)
+  message(header)
+
+  # perform bootstrap
  bootstrap(version, libpath)

+  # exit early if we're just testing bootstrap
+  if (!is.na(Sys.getenv("RENV_BOOTSTRAP_INSTALL_ONLY", unset = NA)))
+    return(TRUE)
+
  # try again to load
  if (requireNamespace("renv", lib.loc = libpath, quietly = TRUE)) {
-    message("Successfully installed and loaded renv ", version, ".")
+    message("* Successfully installed and loaded renv ", version, ".")
    return(renv::load())
  }