support newer conda

pyenv-virtualenvs could not list conda environments & pyenv shell would only activate the base conda environment
the conda detection criteria of testing the presence of `conda` or `activate` files under `$(pyenv root)/versions/$version/bin` appears to be the culprit, since newer environments no longer include these files: those files reside in the base conda environment
- add detection criteria of `$(pyenv root)/versions/$version/conda-meta`
- compute the real prefix to the base environment from `realpath $(realpath $(pyenv root)/versions/$version)/../..`
- to allow that, enhance substitute `realpath` in `pyenv-virtualenvs` to reduce relative paths `.` & `..`, and factor that code out to a file under `libexec` for reuse
- hook `which` to locate conda from the real prefix

bin/pyenv-sh-activate

@@ -177,7 +177,8 @@ EOS
 esac
 
 # anaconda/miniconda
-if [ -x "${prefix}/bin/conda" ]; then
+if [ -d "${prefix}/conda-meta" ] ||
+     [ -x "${prefix}/bin/conda" ]; then
   if [[ "${prefix}" != "${prefix%/envs/*}" ]]; then
     CONDA_DEFAULT_ENV="${venv##*/envs/}"
   else
@@ -233,7 +234,8 @@ EOS
 fi
 
 # conda package anaconda/miniconda scripts (#173)
-if [ -x "${prefix}/bin/conda" ]; then
+if [ -d "${prefix}/conda-meta" ] ||
+     [ -x "${prefix}/bin/conda" ]; then
   shopt -s nullglob
   case "${shell}" in
   fish )

bin/pyenv-sh-deactivate

@@ -59,7 +59,8 @@ if [ -n "$PYENV_VIRTUALENV_VERBOSE_ACTIVATE" ]; then
 fi
 
 # conda package anaconda/miniconda scripts (#173)
-if [ -x "${prefix}/bin/conda" ]; then
+if [ -d "${prefix}/conda-meta" ] ||
+     [ -x "${prefix}/bin/conda" ]; then
   shopt -s nullglob
   case "${shell}" in
   fish )

bin/pyenv-virtualenv-prefix

@@ -6,6 +6,7 @@
 
 set -e
 [ -n "$PYENV_DEBUG" ] && set -x
+. "${BASH_SOURCE%/*}"/../libexec/pyenv-virtualenv-realpath
 
 if [ -z "$PYENV_ROOT" ]; then
   PYENV_ROOT="${HOME}/.pyenv"
@@ -19,6 +20,15 @@ else
   IFS=: versions=($(pyenv-version-name))
 fi
 
+append_virtualenv_prefix() {
+  if [ -d "${VIRTUALENV_PREFIX_PATH}" ]; then
+    VIRTUALENV_PREFIX_PATHS=("${VIRTUALENV_PREFIX_PATHS[@]}" "${VIRTUALENV_PREFIX_PATH:-${PYENV_PREFIX_PATH}}")
+  else
+    echo "pyenv-virtualenv: version \`${version}' is not a virtualenv" 1>&2
+    exit 1
+  fi
+}
+
 VIRTUALENV_PREFIX_PATHS=()
 for version in "${versions[@]}"; do
   if [ "$version" = "system" ]; then
@@ -55,12 +65,11 @@ for version in "${versions[@]}"; do
           fi
         fi
       fi
-      if [ -d "${VIRTUALENV_PREFIX_PATH}" ]; then
-        VIRTUALENV_PREFIX_PATHS=("${VIRTUALENV_PREFIX_PATHS[@]}" "${VIRTUALENV_PREFIX_PATH:-${PYENV_PREFIX_PATH}}")
-      else
-        echo "pyenv-virtualenv: version \`${version}' is not a virtualenv" 1>&2
-        exit 1
-      fi
+      append_virtualenv_prefix
+    elif [ -d "${PYENV_PREFIX_PATH}/conda-meta" ]; then
+      # conda
+      VIRTUALENV_PREFIX_PATH="$(realpath "${PYENV_PREFIX_PATH}"/../..)"
+      append_virtualenv_prefix
     else
       echo "pyenv-virtualenv: version \`${version}' is not a virtualenv" 1>&2
       exit 1

bin/pyenv-virtualenvs

@@ -7,6 +7,7 @@
 
 set -e
 [ -n "$PYENV_DEBUG" ] && set -x
+. "${BASH_SOURCE%/*}"/../libexec/pyenv-virtualenv-realpath
 
 if [ -z "$PYENV_ROOT" ]; then
   PYENV_ROOT="${HOME}/.pyenv"
@@ -32,38 +33,6 @@ done
 
 versions_dir="${PYENV_ROOT}/versions"
 
-if ! enable -f "${BASH_SOURCE%/*}"/../libexec/pyenv-realpath.dylib realpath 2>/dev/null; then
-  if [ -n "$PYENV_NATIVE_EXT" ]; then
-    echo "pyenv: failed to load \`realpath' builtin" >&2
-    exit 1
-  fi
-
-  READLINK=$(type -p greadlink readlink | head -1)
-  if [ -z "$READLINK" ]; then
-    echo "pyenv: cannot find readlink - are you missing GNU coreutils?" >&2
-    exit 1
-  fi
-
-  resolve_link() {
-    $READLINK "$1"
-  }
-
-  realpath() {
-    local cwd="$PWD"
-    local path="$1"
-    local name
-
-    while [ -n "$path" ]; do
-      name="${path##*/}"
-      [ "$name" = "$path" ] || cd "${path%/*}"
-      path="$(resolve_link "$name" || true)"
-    done
-
-    echo "${PWD}/$name"
-    cd "$cwd"
-  }
-fi
-
 if [ -d "$versions_dir" ]; then
   versions_dir="$(realpath "$versions_dir")"
 fi

etc/pyenv.d/which/conda.bash

@@ -0,0 +1,11 @@
+# newer versions of conda share programs from the real prefix
+# this hook tries to find the executable there
+
+if [ ! -x "${PYENV_COMMAND_PATH}" ] && [[ "${PYENV_COMMAND_PATH##*/}" == "conda" ]]; then
+  if [ -d "${PYENV_ROOT}/versions/${version}/conda-meta" ]; then
+    conda_command_path="$(pyenv-virtualenv-prefix "$version")"/bin/"${PYENV_COMMAND_PATH##*/}"
+    if [ -x "${conda_command_path}" ]; then
+      PYENV_COMMAND_PATH="${conda_command_path}"
+    fi
+  fi
+fi

libexec/pyenv-virtualenv-realpath

@@ -0,0 +1,50 @@
+#!/usr/bin/env bash
+# Summary: Substitute realpath if unavailable as a builtin or file
+# Usage: . pyenv-virtualenv-realpath
+
+if ! {
+    enable -f "${BASH_SOURCE%/*}"/../libexec/pyenv-realpath.dylib realpath ||
+      type realpath
+  } >/dev/null 2>&1; then
+  if [ -n "$PYENV_NATIVE_EXT" ]; then
+    echo "pyenv: failed to load \`realpath' builtin" >&2
+    exit 1
+  fi
+
+  READLINK=$(type -p greadlink readlink | head -1)
+  if [ -z "$READLINK" ]; then
+    echo "pyenv: cannot find readlink - are you missing GNU coreutils?" >&2
+    exit 1
+  fi
+
+  resolve_link() {
+    $READLINK "$1"
+  }
+
+  realpath() {
+    local f="$*" \
+          name dir
+    [[ $f ]] || {
+      >&2 echo ${FUNCNAME[0]}: missing operand
+      return
+    }
+    while [[ -L $f ]]; do
+      f="$(resolve_link "$f")"
+    done
+    if [[ ! -d $f ]]; then
+      name="/${f##*/}"
+      # parent?
+      dir="${f%/*}"
+      if [[ $dir == $f ]]; then
+        #lacks /: parent is current directory
+        f="$PWD"
+      else
+        f="$dir"
+      fi
+    fi
+    #absolute directory
+    dir="$(cd "$f"
+           pwd)"
+    echo "$dir$name"
+  }
+fi