MAINT: qiime2/q2cli -> rachis/rachis-cli name change

.gitignore

@@ -77,4 +77,4 @@ runinfo
 _version.py
 
 # Built vendored view
-q2cli/assets/view
+rachis_cli/assets/view

Makefile

@@ -17,7 +17,7 @@ vendor-view: all
 	git submodule update && \
 	cd q2view && \
 	npm install --no-save && \
-	npm run vendor --VENDOR_DIR=../q2cli/assets/view
+	npm run vendor --VENDOR_DIR=../rachis_cli/assets/view
 
 # install pytest-xdist plugin for the `-n auto` argument.
 mystery-stew: all
@@ -26,16 +26,16 @@ mystery-stew: all
 install: vendor-view all
 	$(PYTHON) -m pip install -v . && \
 	mkdir -p $(PREFIX)/etc/conda/activate.d && \
-	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
+	cp hooks/50_activate_rachis_cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 dev: dev-no-view vendor-view all
 
 dev-no-view: all
 	pip install -e . && \
 	mkdir -p $(PREFIX)/etc/conda/activate.d && \
-	cp hooks/50_activate_q2cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
+	cp hooks/50_activate_rachis_cli_tab_completion.sh $(PREFIX)/etc/conda/activate.d/
 
 clean: distclean
-	rm -rf ./q2cli/assets
+	rm -rf ./rachis_cli/assets
 
 distclean: ;

README.md

@@ -1,13 +1,12 @@
-# q2cli
+# rachis-cli
 
-![](https://github.com/qiime2/q2cli/workflows/ci-dev/badge.svg)
+![](https://github.com/rachis-org/rachis-cli/workflows/ci-dev/badge.svg)
 
-A [click-based](http://click.pocoo.org/) command line interface for [QIIME
-2](https://github.com/qiime2/qiime2).
+A [click-based](http://click.pocoo.org/) command line interface for [rachis](https://github.com/rachis-org/rachis).
 
 ## Installation and getting help
 
-Visit https://qiime2.org to learn more about q2cli and the QIIME 2 project.
+Visit https://qiime2.org to learn more about rachis-cli and the rachis project.
 
 ## Enabling tab completion
 
@@ -17,7 +16,7 @@ To enable tab completion in Bash, run the following command or add it to your
 `.bashrc`/`.bash_profile`:
 
 ```bash
-source tab-qiime
+source tab-rachis
 ```
 
 ### ZSH
@@ -26,5 +25,5 @@ To enable tab completion in ZSH, run the following commands or add them to your
 `.zshrc`:
 
 ```bash
-autoload -Uz compinit && compinit && autoload bashcompinit && bashcompinit && source tab-qiime
+autoload -Uz compinit && compinit && autoload bashcompinit && bashcompinit && source tab-rachis
 ```

bin/tab-rachis

@@ -0,0 +1,97 @@
+#!/usr/bin/env bash
+
+# Shell completion for every rachis-cli front-end installed in this
+# environment (e.g. `rachis`, `qiime`, and `mosh` in a MOSHPIT deployment).
+#
+# Front-ends advertise themselves through the `rachis.cli_commands` entry
+# point group; see `rachis_cli.util.get_cli_command_names`.
+#
+# This script is intended to be sourced by the conda activation hook, or on
+# the command-line/in .bashrc/.bash_profile:
+#
+#     source tab-rachis
+#
+# NOTE: this file is always sourced, never executed, so its contents must be
+# valid in both bash and zsh (the shebang above is decorative).
+
+# The cached completion script's path and the set of front-end command names
+# are both fixed for the life of an activation, so they are resolved here once
+# in a single interpreter start - rather than on every <tab>. If rachis-cli
+# isn't installed, or is an incompatible version, this yields nothing and no
+# completion is registered.
+_rachis_meta="$(python -c "import rachis_cli.util as u
+print(u.get_completion_path())
+print('\n'.join(u.get_cli_command_names()))" 2> /dev/null)"
+
+if [ -n "${_rachis_meta}" ]; then
+  _RACHIS_COMPLETION_PATH="${_rachis_meta%%$'\n'*}"
+  _rachis_names="${_rachis_meta#*$'\n'}"
+
+  # `${var#*<newline>}` yields the string unchanged when it holds no newline,
+  # which is what a deployment reporting no front-ends looks like: the empty
+  # trailing line is stripped by the command substitution above.
+  if [ "${_rachis_names}" = "${_rachis_meta}" ]; then
+    _rachis_names=""
+  fi
+
+  # Fall back to the front-ends provided by rachis-cli itself if the entry
+  # point metadata is missing (e.g. an uninstalled source checkout).
+  if [ -z "${_rachis_names}" ]; then
+    _rachis_names="rachis"
+  fi
+
+  # NOTE: `_RACHIS_COMPLETION_PATH` is intentionally left set in the shell -
+  # the completion function below reads it every time it runs.
+  _rachis_completion()
+  {
+    # If the completion script exists, attempt completion by invoking the
+    # script in a subshell, supplying COMP_WORDS and COMP_CWORD. Capture the
+    # output as the completion reply. If the completion script failed, don't
+    # attempt completion.
+    if [[ -f "${_RACHIS_COMPLETION_PATH}" ]] ; then
+      COMPREPLY=( $(COMP_WORDS="${COMP_WORDS[*]}" COMP_CWORD="${COMP_CWORD}" \
+                    "${_RACHIS_COMPLETION_PATH}" 2> /dev/null) )
+
+      if [[ $? != 0 ]]; then
+        unset COMPREPLY
+      fi
+    else
+      unset COMPREPLY
+    fi
+
+    return 0
+  }
+
+  # Register the completion function against each installed front-end.
+  #
+  # NOTE: the iteration is over a command substitution rather than over
+  # `${_rachis_names}` directly because zsh does not word-split unquoted
+  # parameter expansions - passing the list as one argument would register a
+  # single command whose name is the entire list.
+  _rachis_first=""
+  for _rachis_cmd in $(printf '%s\n' "${_rachis_names}"); do
+    # Enable default readline and bash completion behavior when
+    # `_rachis_completion` doesn't have a reply.
+    complete -F _rachis_completion -o default -o bashdefault "${_rachis_cmd}"
+
+    if [ -z "${_rachis_first}" ]; then
+      _rachis_first="${_rachis_cmd}"
+    fi
+  done
+
+  # Execute one of the front-ends (any command will do) so that tab-completion
+  # will work out-of-the-box (e.g. with a fresh installation of rachis-cli).
+  # Running a command will create or refresh the cache if necessary, which
+  # contains the actual completion script.
+  #
+  # Ignore stdout to avoid displaying help text to users enabling
+  # tab-completion. stderr displays the note about cache refreshing, as that
+  # can take a few moments to complete.
+  if [ -n "${_rachis_first}" ]; then
+    "${_rachis_first}" &> /dev/null
+  fi
+
+  unset _rachis_names _rachis_cmd _rachis_first
+fi
+
+unset _rachis_meta

conda-recipe/meta.yaml

@@ -1,12 +1,12 @@
 package:
-  name: q2cli
+  name: rachis-cli
   version: {{ PLUGIN_VERSION }}
 source:
   path: ..
 build:
   script: make install
   entry_points:
-  - qiime=q2cli.__main__:qiime
+  - rachis=rachis_cli.__main__:rachis
 requirements:
   host:
   - python {{ python }}
@@ -18,24 +18,24 @@ requirements:
   - python {{ python }}
   - setuptools
   - click {{ click }}
-  - qiime2 >={{ qiime2 }}
+  - rachis >={{ rachis }}
   - q2templates >={{ q2templates }}
   build:
   - python {{ python }}
   - setuptools
   - versioningit
 test:
   requires:
-  - qiime2 >={{ qiime2 }}
+  - rachis >={{ rachis }}
   - q2templates >={{ q2templates }}
   - pytest
   - pytest-xdist
   - q2-mystery-stew
   imports:
-  - q2cli
+  - rachis_cli
   commands:
-  - Q2CLIDEV=1 QIIMETEST= qiime --help
-  - Q2CLIDEV=1 QIIMETEST= py.test --pyargs q2cli
+  - Q2CLIDEV=1 QIIMETEST= rachis --help
+  - Q2CLIDEV=1 QIIMETEST= py.test --pyargs rachis_cli
 about:
   home: https://qiime2.org
   license: BSD-3-Clause

hooks/50_activate_q2cli_tab_completion.sh → hooks/50_activate_rachis_cli_tab_completion.sh

@@ -1,5 +1,5 @@
 if [ -n "${ZSH_VERSION-}" ]; then
-  autoload -Uz compinit && compinit && autoload bashcompinit && bashcompinit && source tab-qiime
+  autoload -Uz compinit && compinit && autoload bashcompinit && bashcompinit && source tab-rachis
 elif [ -n "${BASH_VERSION-}" ]; then
-  source tab-qiime
+  source tab-rachis
 fi

pyproject.toml

@@ -1,5 +1,5 @@
 [project]
-name = "q2cli"
+name = "rachis-cli"
 authors = [
     { name = "None", email = "developers@qiime2.org" }
 ]
@@ -10,13 +10,16 @@ dynamic = ["version"]
 
 [project.urls]
 Homepage = "https://qiime2.org"
-Repository = "https://github.com/qiime2/q2cli"
+Repository = "https://github.com/rachis-org/rachis-cli"
 
 [project.scripts]
-"qiime" = "q2cli.__main__:qiime"
+"rachis" = "rachis_cli.__main__:rachis"
 
-[project.entry-points.'qiime2.usage_drivers']
-"cli" = "q2cli.core.usage:ReplayCLIUsage"
+[project.entry-points.'rachis.cli_commands']
+"rachis" = "rachis_cli.__main__:rachis"
+
+[project.entry-points.'rachis.usage_drivers']
+"cli" = "rachis_cli.core.usage:ReplayCLIUsage"
 
 [build-system]
 requires = [
@@ -40,17 +43,17 @@ dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
 
 [tool.versioningit.write]
-file = "q2cli/_version.py"
+file = "rachis_cli/_version.py"
 
 [tool.setuptools]
 include-package-data = true
 script-files = [
-    "bin/tab-qiime"
+    "bin/tab-rachis"
 ]
 
 [tool.setuptools.packages.find]
 where = ["."]
-include = ["q2cli*"]
+include = ["rachis_cli*"]
 
 [tool.setuptools.package-data]
-q2cli = ["**/*"]
+rachis_cli = ["**/*"]

q2cli/__main__.py → rachis_cli/__main__.py

@@ -8,40 +8,41 @@
 
 import click
 
-import q2cli.commands
+import rachis_cli.commands
 
 
 ROOT_COMMAND_HELP = """\
-QIIME 2 command-line interface (q2cli)
---------------------------------------
+rachis command-line interface (rachis-cli)
+------------------------------------------
 
-To get help with QIIME 2, visit https://qiime2.org.
+To get help with rachis, visit https://qiime2.org.
 
 To enable tab completion in Bash, run the following command or add it to your \
 .bashrc/.bash_profile:
 
-    source tab-qiime
+    source tab-rachis
 
 To enable tab completion in ZSH, run the following commands or add them to \
 your .zshrc:
 
 \b
     autoload -Uz compinit && compinit
     autoload bashcompinit && bashcompinit
-    source tab-qiime
+    source tab-rachis
 
 """
 
 
 # Entry point for CLI
-@click.command(cls=q2cli.commands.RootCommand, invoke_without_command=True,
+@click.command(cls=rachis_cli.commands.RootCommand,
+               invoke_without_command=True,
                no_args_is_help=True, help=ROOT_COMMAND_HELP)
-@click.version_option(prog_name='q2cli',
-                      message='%(prog)s version %(version)s\nRun `qiime info` '
-                              'for more version details.')
-def qiime():
+@click.version_option(prog_name='rachis-cli',
+                      message='%(prog)s version %(version)s\nRun `rachis info`'
+                              ' for more version details.')
+def rachis():
     pass
 
 
 if __name__ == '__main__':
-    qiime()
+    rachis()