From bc77bfd8f3d6cf4fcbf65beb5493e85944f3d7f0 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sat, 14 May 2022 11:28:51 -0700
Subject: [PATCH 01/15] bootstrap-conda: Write an additional comment

---
 bootstrap-conda | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bootstrap-conda b/bootstrap-conda
index 92aea50f939..7dd6b701128 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -59,6 +59,7 @@ for pkg in $BOOTSTRAP_PACKAGES; do
     echo "  - $pkg" >> environment.yml
 done
 sed 's/name: sage-build/name: sage/' environment.yml > src/environment.yml
+echo "  # Additional packages providing all dependencies for the Sage library" >> src/environment.yml
 for pkg in $SAGELIB_SYSTEM_PACKAGES; do
     echo "  - $pkg" >> src/environment.yml
 done

From 4c2adf7e74f3783564bd88a78d786bc35c346932 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sat, 14 May 2022 11:59:08 -0700
Subject: [PATCH 02/15] bootstrap-conda: Rewrite using fewer redirects

---
 bootstrap-conda | 76 +++++++++++++++++++++++++++++--------------------
 1 file changed, 45 insertions(+), 31 deletions(-)

diff --git a/bootstrap-conda b/bootstrap-conda
index 7dd6b701128..3cb23bfbac9 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -46,36 +46,50 @@ for PKG_BASE in $(sage-package list --has-file distros/conda.txt); do
     fi
 done
 echo >&2 $0:$LINENO: generate conda enviroment files
-echo "name: sage-build" >  environment.yml
-echo "channels:"        >> environment.yml
-echo "  - conda-forge"  >> environment.yml
-echo "  - nodefaults"   >> environment.yml
-echo "dependencies:"    >> environment.yml
-for pkg in $SYSTEM_PACKAGES; do
-    echo "  - $pkg" >> environment.yml
-done
-echo "  # Packages needed for ./bootstrap" >> environment.yml
-for pkg in $BOOTSTRAP_PACKAGES; do
-    echo "  - $pkg" >> environment.yml
-done
-sed 's/name: sage-build/name: sage/' environment.yml > src/environment.yml
-echo "  # Additional packages providing all dependencies for the Sage library" >> src/environment.yml
-for pkg in $SAGELIB_SYSTEM_PACKAGES; do
-    echo "  - $pkg" >> src/environment.yml
-done
-sed 's/name: sage/name: sage-dev/' src/environment.yml > src/environment-dev.yml
-echo "  # Additional dev tools" >> src/environment-dev.yml
-echo "  - openssh" >> src/environment-dev.yml
-echo "  - pycodestyle" >> src/environment-dev.yml
-echo "  - pytest" >> src/environment-dev.yml
+(
+    echo "name: sage-build"
+    echo "channels:"
+    echo "  - conda-forge"
+    echo "  - nodefaults"
+    echo "dependencies:"
+    for pkg in $SYSTEM_PACKAGES; do
+        echo "  - $pkg"
+    done
+    echo "  # Packages needed for ./bootstrap"
+    for pkg in $BOOTSTRAP_PACKAGES; do
+        echo "  - $pkg"
+    done
+) > environment.yml
 
-cp environment.yml environment-optional.yml
-    echo "  # optional packages" >> environment-optional.yml
-for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
-    echo "  - $pkg" >> environment-optional.yml
+(
+    sed 's/name: sage-build/name: sage/' environment.yml
+    echo "  # Additional packages providing all dependencies for the Sage library"
+    for pkg in $SAGELIB_SYSTEM_PACKAGES; do
+        echo "  - $pkg"
     done
-cp src/environment.yml src/environment-optional.yml
-    echo "  # optional packages" >> src/environment-optional.yml
-for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
-    echo "  - $pkg" >> src/environment-optional.yml
-done
+) > src/environment.yml
+
+DEVELOP_SYSTEM_PACKAGES="openssh pycodestyle pytest"
+(
+    sed 's/name: sage/name: sage-dev/' src/environment.yml
+    echo "  # Additional dev tools"
+    for pkg in $DEVELOP_SYSTEM_PACKAGES; do
+        echo "  - $pkg"
+    done
+) > src/environment-dev.yml
+
+(
+    cat environment.yml
+    echo "  # optional packages"
+    for pkg in $OPTIONAL_SYSTEM_PACKAGES; do
+        echo "  - $pkg"
+    done
+) > environment-optional.yml
+
+(
+    cat src/environment.yml
+    echo "  # optional packages"
+    for pkg in $OPTIONAL_SYSTEM_PACKAGES $SAGELIB_OPTIONAL_SYSTEM_PACKAGES; do
+        echo "  - $pkg"
+    done
+) > src/environment-optional.yml

From ac2c48db84c1a59e333552e5abfcdc3229fb9084 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 16 May 2022 15:10:34 -0700
Subject: [PATCH 03/15] build/pkgs/git_trac_command: New

---
 build/pkgs/git_trac_command/SPKG.rst         | 14 ++++++++++++++
 build/pkgs/git_trac_command/requirements.txt |  1 +
 build/pkgs/git_trac_command/trees.txt        |  1 +
 build/pkgs/git_trac_command/type             |  1 +
 4 files changed, 17 insertions(+)
 create mode 100644 build/pkgs/git_trac_command/SPKG.rst
 create mode 100644 build/pkgs/git_trac_command/requirements.txt
 create mode 100644 build/pkgs/git_trac_command/trees.txt
 create mode 100644 build/pkgs/git_trac_command/type

diff --git a/build/pkgs/git_trac_command/SPKG.rst b/build/pkgs/git_trac_command/SPKG.rst
new file mode 100644
index 00000000000..d8da01bd818
--- /dev/null
+++ b/build/pkgs/git_trac_command/SPKG.rst
@@ -0,0 +1,14 @@
+git_trac_command: Provides the subcommand "git trac"
+====================================================
+
+Description
+-----------
+
+This module implements a subcommand ``git trac``.
+See https://doc.sagemath.org/html/en/developer/git_trac.html
+
+
+Upstream Contact
+----------------
+
+https://github.com/sagemath/git-trac-command
diff --git a/build/pkgs/git_trac_command/requirements.txt b/build/pkgs/git_trac_command/requirements.txt
new file mode 100644
index 00000000000..4f36b5eae53
--- /dev/null
+++ b/build/pkgs/git_trac_command/requirements.txt
@@ -0,0 +1 @@
+git+https://github.com/sagemath/git-trac-command
diff --git a/build/pkgs/git_trac_command/trees.txt b/build/pkgs/git_trac_command/trees.txt
new file mode 100644
index 00000000000..b268580307d
--- /dev/null
+++ b/build/pkgs/git_trac_command/trees.txt
@@ -0,0 +1 @@
+# Users should install this manually in their environment. It should not be installed in SAGE_VENV
diff --git a/build/pkgs/git_trac_command/type b/build/pkgs/git_trac_command/type
new file mode 100644
index 00000000000..134d9bc32d5
--- /dev/null
+++ b/build/pkgs/git_trac_command/type
@@ -0,0 +1 @@
+optional

From 4a0b6f47a798a00643f51827da229e913cd8680d Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 16 May 2022 16:44:16 -0700
Subject: [PATCH 04/15] bootstrap-conda: Also generate pip: lines

---
 bootstrap-conda | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)

diff --git a/bootstrap-conda b/bootstrap-conda
index 3cb23bfbac9..260c8751312 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -93,3 +93,21 @@ DEVELOP_SYSTEM_PACKAGES="openssh pycodestyle pytest"
         echo "  - $pkg"
     done
 ) > src/environment-optional.yml
+(
+    echo >&4 "  - pip:"
+    echo >&5 "  - pip:"
+    for PKG_BASE in $(sage-package list --has-file requirements.txt --no-file distros/conda.txt); do
+        PKG_SCRIPTS=build/pkgs/$PKG_BASE
+        SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
+        PKG_TYPE=$(cat $PKG_SCRIPTS/type)
+        if [ -n "PKG_SYSTEM_PACKAGES" ]; then
+            case "$PKG_BASE:$PKG_TYPE" in
+                $DEVELOP_SPKG_PATTERN:*) FD=4;;
+                *)                       FD=5;;
+            esac
+            ${STRIP_COMMENTS} $SYSTEM_PACKAGES_FILE | while read -r line; do
+                [ -n "$line" ] && echo >&$FD "    - $line"
+            done
+        fi
+    done
+) 4>> src/environment-dev.yml 5>> src/environment-optional.yml

From ef01ba46603937842a3a6d984c3bf5baa8e8997d Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 16 May 2022 17:08:24 -0700
Subject: [PATCH 05/15] bootstrap-conda: Do not include packages that declare
 SAGERUNTIME as a dependency

---
 bootstrap-conda                       | 4 +++-
 build/pkgs/sage_flatsurf/dependencies | 2 +-
 build/pkgs/slabbe/dependencies        | 2 +-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/bootstrap-conda b/bootstrap-conda
index 260c8751312..3337bca58d3 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -100,7 +100,9 @@ DEVELOP_SYSTEM_PACKAGES="openssh pycodestyle pytest"
         PKG_SCRIPTS=build/pkgs/$PKG_BASE
         SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
         PKG_TYPE=$(cat $PKG_SCRIPTS/type)
-        if [ -n "PKG_SYSTEM_PACKAGES" ]; then
+        if grep -q SAGERUNTIME $PKG_SCRIPTS/dependencies 2>/dev/null; then
+            : # cannot install packages that depend on the Sage library
+        else
             case "$PKG_BASE:$PKG_TYPE" in
                 $DEVELOP_SPKG_PATTERN:*) FD=4;;
                 *)                       FD=5;;
diff --git a/build/pkgs/sage_flatsurf/dependencies b/build/pkgs/sage_flatsurf/dependencies
index 951fd368f40..4c62fdd4fef 100644
--- a/build/pkgs/sage_flatsurf/dependencies
+++ b/build/pkgs/sage_flatsurf/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN) surface_dynamics
+$(PYTHON) | $(PYTHON_TOOLCHAIN) surface_dynamics $(SAGERUNTIME)
 
 ----------
 All lines of this file are ignored except the first.
diff --git a/build/pkgs/slabbe/dependencies b/build/pkgs/slabbe/dependencies
index 0738c2d7777..05ba0d8954b 100644
--- a/build/pkgs/slabbe/dependencies
+++ b/build/pkgs/slabbe/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) | $(PYTHON_TOOLCHAIN)
+$(PYTHON) | $(PYTHON_TOOLCHAIN) $(SAGERUNTIME)
 
 ----------
 All lines of this file are ignored except the first.

From 8e511f232585f98f18befe40945be71964b21d41 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sun, 29 May 2022 15:43:21 -0700
Subject: [PATCH 06/15] bootstrap-conda: Hardcode git_trac_command as a devel
 package

---
 bootstrap-conda | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bootstrap-conda b/bootstrap-conda
index 3337bca58d3..d8c76e3f1ee 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -8,6 +8,7 @@ export PATH="$(pwd)/build/bin:$PATH"
 
 STRIP_COMMENTS="sed s/#.*//;"
 RECOMMENDED_SPKG_PATTERN="@(_recommended$(for a in $(head -n 1 build/pkgs/_recommended/dependencies); do echo -n "|"$a; done))"
+DEVELOP_SPKG_PATTERN="git_trac_command"
 
 BOOTSTRAP_PACKAGES=$(echo $(${STRIP_COMMENTS} build/pkgs/_bootstrap/distros/conda.txt))
 SYSTEM_PACKAGES=

From 2019f4791f0bc6edf6c9f35a1ae618206d02623b Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Wed, 29 Jun 2022 13:51:30 -0700
Subject: [PATCH 07/15] bootstrap-conda: Also check dependencies_order_only

---
 bootstrap-conda | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bootstrap-conda b/bootstrap-conda
index d8c76e3f1ee..2631dc8723f 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -101,7 +101,7 @@ DEVELOP_SYSTEM_PACKAGES="openssh pycodestyle pytest"
         PKG_SCRIPTS=build/pkgs/$PKG_BASE
         SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
         PKG_TYPE=$(cat $PKG_SCRIPTS/type)
-        if grep -q SAGERUNTIME $PKG_SCRIPTS/dependencies 2>/dev/null; then
+        if grep -q SAGERUNTIME $PKG_SCRIPTS/dependencies $PKG_SCRIPTS/dependencies_order_only 2>/dev/null; then
             : # cannot install packages that depend on the Sage library
         else
             case "$PKG_BASE:$PKG_TYPE" in

From a004e002d8353e08e5d1f7d6601ac2d434c50f30 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 20:24:59 -0700
Subject: [PATCH 08/15] build/pkgs/python_build/distros/conda.txt: New

---
 build/pkgs/python_build/distros/conda.txt | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 build/pkgs/python_build/distros/conda.txt

diff --git a/build/pkgs/python_build/distros/conda.txt b/build/pkgs/python_build/distros/conda.txt
new file mode 100644
index 00000000000..378eac25d31
--- /dev/null
+++ b/build/pkgs/python_build/distros/conda.txt
@@ -0,0 +1 @@
+build

From d508d7bff7e4d2fce3e097b58ba4726aa973b65d Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 20:58:57 -0700
Subject: [PATCH 09/15] build/pkgs: Add many more distros/conda.txt files

---
 build/pkgs/appnope/distros/conda.txt           | 1 +
 build/pkgs/beniget/conda.txt                   | 1 +
 build/pkgs/distlib/distros/conda.txt           | 1 +
 build/pkgs/fastjsonschema/distros/conda.txt    | 1 +
 build/pkgs/hatchling/distros/conda.txt         | 1 +
 build/pkgs/matplotlib_inline/distros/conda.txt | 1 +
 build/pkgs/nest_asyncio/distros/conda.txt      | 1 +
 build/pkgs/ply/distros/conda.txt               | 1 +
 build/pkgs/pure_eval/distros/conda.txt         | 1 +
 build/pkgs/py/distros/conda.txt                | 1 +
 build/pkgs/soupsieve/distros/conda.txt         | 1 +
 build/pkgs/stack_data/distros/conda.txt        | 1 +
 build/pkgs/toml/distros/conda.txt              | 1 +
 13 files changed, 13 insertions(+)
 create mode 100644 build/pkgs/appnope/distros/conda.txt
 create mode 100644 build/pkgs/beniget/conda.txt
 create mode 100644 build/pkgs/distlib/distros/conda.txt
 create mode 100644 build/pkgs/fastjsonschema/distros/conda.txt
 create mode 100644 build/pkgs/hatchling/distros/conda.txt
 create mode 100644 build/pkgs/matplotlib_inline/distros/conda.txt
 create mode 100644 build/pkgs/nest_asyncio/distros/conda.txt
 create mode 100644 build/pkgs/ply/distros/conda.txt
 create mode 100644 build/pkgs/pure_eval/distros/conda.txt
 create mode 100644 build/pkgs/py/distros/conda.txt
 create mode 100644 build/pkgs/soupsieve/distros/conda.txt
 create mode 100644 build/pkgs/stack_data/distros/conda.txt
 create mode 100644 build/pkgs/toml/distros/conda.txt

diff --git a/build/pkgs/appnope/distros/conda.txt b/build/pkgs/appnope/distros/conda.txt
new file mode 100644
index 00000000000..010137fae0e
--- /dev/null
+++ b/build/pkgs/appnope/distros/conda.txt
@@ -0,0 +1 @@
+appnope
diff --git a/build/pkgs/beniget/conda.txt b/build/pkgs/beniget/conda.txt
new file mode 100644
index 00000000000..8b5faaea7c2
--- /dev/null
+++ b/build/pkgs/beniget/conda.txt
@@ -0,0 +1 @@
+beniget
diff --git a/build/pkgs/distlib/distros/conda.txt b/build/pkgs/distlib/distros/conda.txt
new file mode 100644
index 00000000000..f68bb07272d
--- /dev/null
+++ b/build/pkgs/distlib/distros/conda.txt
@@ -0,0 +1 @@
+distlib
diff --git a/build/pkgs/fastjsonschema/distros/conda.txt b/build/pkgs/fastjsonschema/distros/conda.txt
new file mode 100644
index 00000000000..7a8bdf5369b
--- /dev/null
+++ b/build/pkgs/fastjsonschema/distros/conda.txt
@@ -0,0 +1 @@
+python-fastjsonschema
diff --git a/build/pkgs/hatchling/distros/conda.txt b/build/pkgs/hatchling/distros/conda.txt
new file mode 100644
index 00000000000..1685d03c212
--- /dev/null
+++ b/build/pkgs/hatchling/distros/conda.txt
@@ -0,0 +1 @@
+hatchling
diff --git a/build/pkgs/matplotlib_inline/distros/conda.txt b/build/pkgs/matplotlib_inline/distros/conda.txt
new file mode 100644
index 00000000000..7b78209dd96
--- /dev/null
+++ b/build/pkgs/matplotlib_inline/distros/conda.txt
@@ -0,0 +1 @@
+matplotlib-inline
diff --git a/build/pkgs/nest_asyncio/distros/conda.txt b/build/pkgs/nest_asyncio/distros/conda.txt
new file mode 100644
index 00000000000..875c8427e6c
--- /dev/null
+++ b/build/pkgs/nest_asyncio/distros/conda.txt
@@ -0,0 +1 @@
+nest-asyncio
diff --git a/build/pkgs/ply/distros/conda.txt b/build/pkgs/ply/distros/conda.txt
new file mode 100644
index 00000000000..90412f06833
--- /dev/null
+++ b/build/pkgs/ply/distros/conda.txt
@@ -0,0 +1 @@
+ply
diff --git a/build/pkgs/pure_eval/distros/conda.txt b/build/pkgs/pure_eval/distros/conda.txt
new file mode 100644
index 00000000000..e50c81f634f
--- /dev/null
+++ b/build/pkgs/pure_eval/distros/conda.txt
@@ -0,0 +1 @@
+pure_eval
diff --git a/build/pkgs/py/distros/conda.txt b/build/pkgs/py/distros/conda.txt
new file mode 100644
index 00000000000..edfce786a4d
--- /dev/null
+++ b/build/pkgs/py/distros/conda.txt
@@ -0,0 +1 @@
+py
diff --git a/build/pkgs/soupsieve/distros/conda.txt b/build/pkgs/soupsieve/distros/conda.txt
new file mode 100644
index 00000000000..9eb997f7a10
--- /dev/null
+++ b/build/pkgs/soupsieve/distros/conda.txt
@@ -0,0 +1 @@
+soupsieve
diff --git a/build/pkgs/stack_data/distros/conda.txt b/build/pkgs/stack_data/distros/conda.txt
new file mode 100644
index 00000000000..09e7428c13d
--- /dev/null
+++ b/build/pkgs/stack_data/distros/conda.txt
@@ -0,0 +1 @@
+stack_data
diff --git a/build/pkgs/toml/distros/conda.txt b/build/pkgs/toml/distros/conda.txt
new file mode 100644
index 00000000000..bd79a658fe7
--- /dev/null
+++ b/build/pkgs/toml/distros/conda.txt
@@ -0,0 +1 @@
+toml

From 098a8e7a9a473a437a8dc12902fb1571b4450da0 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 21:02:42 -0700
Subject: [PATCH 10/15] build/pkgs: Add some more distros/conda.txt files

---
 build/pkgs/executing/distros/conda.txt | 1 +
 build/pkgs/tzdata/distros/conda.txt    | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 build/pkgs/executing/distros/conda.txt
 create mode 100644 build/pkgs/tzdata/distros/conda.txt

diff --git a/build/pkgs/executing/distros/conda.txt b/build/pkgs/executing/distros/conda.txt
new file mode 100644
index 00000000000..a920f2c56c3
--- /dev/null
+++ b/build/pkgs/executing/distros/conda.txt
@@ -0,0 +1 @@
+executing
diff --git a/build/pkgs/tzdata/distros/conda.txt b/build/pkgs/tzdata/distros/conda.txt
new file mode 100644
index 00000000000..0883ff0705b
--- /dev/null
+++ b/build/pkgs/tzdata/distros/conda.txt
@@ -0,0 +1 @@
+tzdata

From c56aa71a7c48b63754554f9449152197123f6c1c Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 21:03:08 -0700
Subject: [PATCH 11/15] bootstrap-conda: Also add pip lines when
 install-requires.txt is present

---
 bootstrap-conda | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/bootstrap-conda b/bootstrap-conda
index 9ad39468e5d..cc9f02d0ec6 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -97,9 +97,12 @@ DEVELOP_SYSTEM_PACKAGES="openssh pycodestyle pytest"
 (
     echo >&4 "  - pip:"
     echo >&5 "  - pip:"
-    for PKG_BASE in $(sage-package list --has-file requirements.txt --no-file distros/conda.txt); do
+    for PKG_BASE in $(sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt) $(sage-package list :standard: :optional: --has-file install-requires.txt --no-file requirements.txt --no-file distros/conda.txt); do
         PKG_SCRIPTS=build/pkgs/$PKG_BASE
         SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
+        if [ ! -f $SYSTEM_PACKAGES_FILE ]; then
+            SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/install-requires.txt
+        fi
         PKG_TYPE=$(cat $PKG_SCRIPTS/type)
         if grep -q SAGERUNTIME $PKG_SCRIPTS/dependencies $PKG_SCRIPTS/dependencies_order_only 2>/dev/null; then
             : # cannot install packages that depend on the Sage library

From c13eaf1176c9067b220927a4cc57c7bf901c0ef7 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 22:17:24 -0700
Subject: [PATCH 12/15] build/pkgs: Add even more distros/conda.txt files

---
 build/pkgs/appdirs/distros/conda.txt                    | 1 +
 build/pkgs/argon2_cffi/distros/conda.txt                | 1 +
 build/pkgs/asttokens/distros/conda.txt                  | 1 +
 build/pkgs/backports_zoneinfo/distros/conda.txt         | 1 +
 build/pkgs/charset_normalizer/distros/conda.txt         | 1 +
 build/pkgs/cppy/distros/conda.txt                       | 1 +
 build/pkgs/debugpy/distros/conda.txt                    | 1 +
 build/pkgs/deprecation/distros/conda.txt                | 1 +
 build/pkgs/dot2tex/distros/conda.txt                    | 1 +
 build/pkgs/editables/distros/conda.txt                  | 1 +
 build/pkgs/filelock/distros/conda.txt                   | 1 +
 build/pkgs/flit_core/distros/conda.txt                  | 1 +
 build/pkgs/fonttools/distros/conda.txt                  | 1 +
 build/pkgs/gast/distros/conda.txt                       | 1 +
 build/pkgs/idna/distros/conda.txt                       | 1 +
 build/pkgs/importlib_resources/distros/conda.txt        | 1 +
 build/pkgs/jupyter_jsmol/distros/conda.txt              | 1 +
 build/pkgs/jupyterlab_pygments/distros/conda.txt        | 1 +
 build/pkgs/mathics/distros/conda.txt                    | 1 +
 build/pkgs/nbclient/distros/conda.txt                   | 1 +
 build/pkgs/palettable/distros/conda.txt                 | 1 +
 build/pkgs/pathspec/distros/conda.txt                   | 1 +
 build/pkgs/pint/distros/conda.txt                       | 1 +
 build/pkgs/platformdirs/distros/conda.txt               | 1 +
 build/pkgs/pluggy/distros/conda.txt                     | 1 +
 build/pkgs/poetry_core/distros/conda.txt                | 1 +
 build/pkgs/pythran/distros/conda.txt                    | 1 +
 build/pkgs/pytz_deprecation_shim/distros/conda.txt      | 1 +
 build/pkgs/setuptools_scm_git_archive/distros/conda.txt | 1 +
 build/pkgs/texttable/distros/conda.txt                  | 1 +
 build/pkgs/tinycss2/distros/conda.txt                   | 1 +
 build/pkgs/tomli/distros/conda.txt                      | 1 +
 build/pkgs/tomlkit/distros/conda.txt                    | 1 +
 build/pkgs/typing_extensions/distros/conda.txt          | 1 +
 build/pkgs/urllib3/distros/conda.txt                    | 1 +
 build/pkgs/virtualenv/distros/conda.txt                 | 1 +
 36 files changed, 36 insertions(+)
 create mode 100644 build/pkgs/appdirs/distros/conda.txt
 create mode 100644 build/pkgs/argon2_cffi/distros/conda.txt
 create mode 100644 build/pkgs/asttokens/distros/conda.txt
 create mode 100644 build/pkgs/backports_zoneinfo/distros/conda.txt
 create mode 100644 build/pkgs/charset_normalizer/distros/conda.txt
 create mode 100644 build/pkgs/cppy/distros/conda.txt
 create mode 100644 build/pkgs/debugpy/distros/conda.txt
 create mode 100644 build/pkgs/deprecation/distros/conda.txt
 create mode 100644 build/pkgs/dot2tex/distros/conda.txt
 create mode 100644 build/pkgs/editables/distros/conda.txt
 create mode 100644 build/pkgs/filelock/distros/conda.txt
 create mode 100644 build/pkgs/flit_core/distros/conda.txt
 create mode 100644 build/pkgs/fonttools/distros/conda.txt
 create mode 100644 build/pkgs/gast/distros/conda.txt
 create mode 100644 build/pkgs/idna/distros/conda.txt
 create mode 100644 build/pkgs/importlib_resources/distros/conda.txt
 create mode 100644 build/pkgs/jupyter_jsmol/distros/conda.txt
 create mode 100644 build/pkgs/jupyterlab_pygments/distros/conda.txt
 create mode 100644 build/pkgs/mathics/distros/conda.txt
 create mode 100644 build/pkgs/nbclient/distros/conda.txt
 create mode 100644 build/pkgs/palettable/distros/conda.txt
 create mode 100644 build/pkgs/pathspec/distros/conda.txt
 create mode 100644 build/pkgs/pint/distros/conda.txt
 create mode 100644 build/pkgs/platformdirs/distros/conda.txt
 create mode 100644 build/pkgs/pluggy/distros/conda.txt
 create mode 100644 build/pkgs/poetry_core/distros/conda.txt
 create mode 100644 build/pkgs/pythran/distros/conda.txt
 create mode 100644 build/pkgs/pytz_deprecation_shim/distros/conda.txt
 create mode 100644 build/pkgs/setuptools_scm_git_archive/distros/conda.txt
 create mode 100644 build/pkgs/texttable/distros/conda.txt
 create mode 100644 build/pkgs/tinycss2/distros/conda.txt
 create mode 100644 build/pkgs/tomli/distros/conda.txt
 create mode 100644 build/pkgs/tomlkit/distros/conda.txt
 create mode 100644 build/pkgs/typing_extensions/distros/conda.txt
 create mode 100644 build/pkgs/urllib3/distros/conda.txt
 create mode 100644 build/pkgs/virtualenv/distros/conda.txt

diff --git a/build/pkgs/appdirs/distros/conda.txt b/build/pkgs/appdirs/distros/conda.txt
new file mode 100644
index 00000000000..d64bc321a11
--- /dev/null
+++ b/build/pkgs/appdirs/distros/conda.txt
@@ -0,0 +1 @@
+appdirs
diff --git a/build/pkgs/argon2_cffi/distros/conda.txt b/build/pkgs/argon2_cffi/distros/conda.txt
new file mode 100644
index 00000000000..d05a5eb79fb
--- /dev/null
+++ b/build/pkgs/argon2_cffi/distros/conda.txt
@@ -0,0 +1 @@
+argon2-cffi
diff --git a/build/pkgs/asttokens/distros/conda.txt b/build/pkgs/asttokens/distros/conda.txt
new file mode 100644
index 00000000000..7adf4c51fd2
--- /dev/null
+++ b/build/pkgs/asttokens/distros/conda.txt
@@ -0,0 +1 @@
+asttokens
diff --git a/build/pkgs/backports_zoneinfo/distros/conda.txt b/build/pkgs/backports_zoneinfo/distros/conda.txt
new file mode 100644
index 00000000000..5a8be642f33
--- /dev/null
+++ b/build/pkgs/backports_zoneinfo/distros/conda.txt
@@ -0,0 +1 @@
+backports.zoneinfo
diff --git a/build/pkgs/charset_normalizer/distros/conda.txt b/build/pkgs/charset_normalizer/distros/conda.txt
new file mode 100644
index 00000000000..5f964199cd0
--- /dev/null
+++ b/build/pkgs/charset_normalizer/distros/conda.txt
@@ -0,0 +1 @@
+charset-normalizer
diff --git a/build/pkgs/cppy/distros/conda.txt b/build/pkgs/cppy/distros/conda.txt
new file mode 100644
index 00000000000..9d2b4aaeee0
--- /dev/null
+++ b/build/pkgs/cppy/distros/conda.txt
@@ -0,0 +1 @@
+cppy
diff --git a/build/pkgs/debugpy/distros/conda.txt b/build/pkgs/debugpy/distros/conda.txt
new file mode 100644
index 00000000000..2802a6b1b1c
--- /dev/null
+++ b/build/pkgs/debugpy/distros/conda.txt
@@ -0,0 +1 @@
+debugpy
diff --git a/build/pkgs/deprecation/distros/conda.txt b/build/pkgs/deprecation/distros/conda.txt
new file mode 100644
index 00000000000..4ba9b7530ed
--- /dev/null
+++ b/build/pkgs/deprecation/distros/conda.txt
@@ -0,0 +1 @@
+deprecation
diff --git a/build/pkgs/dot2tex/distros/conda.txt b/build/pkgs/dot2tex/distros/conda.txt
new file mode 100644
index 00000000000..4d0a832a550
--- /dev/null
+++ b/build/pkgs/dot2tex/distros/conda.txt
@@ -0,0 +1 @@
+dot2tex
diff --git a/build/pkgs/editables/distros/conda.txt b/build/pkgs/editables/distros/conda.txt
new file mode 100644
index 00000000000..35c51715e64
--- /dev/null
+++ b/build/pkgs/editables/distros/conda.txt
@@ -0,0 +1 @@
+editables
diff --git a/build/pkgs/filelock/distros/conda.txt b/build/pkgs/filelock/distros/conda.txt
new file mode 100644
index 00000000000..83c2e35706e
--- /dev/null
+++ b/build/pkgs/filelock/distros/conda.txt
@@ -0,0 +1 @@
+filelock
diff --git a/build/pkgs/flit_core/distros/conda.txt b/build/pkgs/flit_core/distros/conda.txt
new file mode 100644
index 00000000000..14ccfd92035
--- /dev/null
+++ b/build/pkgs/flit_core/distros/conda.txt
@@ -0,0 +1 @@
+flit-core
diff --git a/build/pkgs/fonttools/distros/conda.txt b/build/pkgs/fonttools/distros/conda.txt
new file mode 100644
index 00000000000..d32bfca1a29
--- /dev/null
+++ b/build/pkgs/fonttools/distros/conda.txt
@@ -0,0 +1 @@
+fonttools
diff --git a/build/pkgs/gast/distros/conda.txt b/build/pkgs/gast/distros/conda.txt
new file mode 100644
index 00000000000..beb259c8453
--- /dev/null
+++ b/build/pkgs/gast/distros/conda.txt
@@ -0,0 +1 @@
+gast
diff --git a/build/pkgs/idna/distros/conda.txt b/build/pkgs/idna/distros/conda.txt
new file mode 100644
index 00000000000..c40472e6fc2
--- /dev/null
+++ b/build/pkgs/idna/distros/conda.txt
@@ -0,0 +1 @@
+idna
diff --git a/build/pkgs/importlib_resources/distros/conda.txt b/build/pkgs/importlib_resources/distros/conda.txt
new file mode 100644
index 00000000000..2b0146fc669
--- /dev/null
+++ b/build/pkgs/importlib_resources/distros/conda.txt
@@ -0,0 +1 @@
+importlib-resources
diff --git a/build/pkgs/jupyter_jsmol/distros/conda.txt b/build/pkgs/jupyter_jsmol/distros/conda.txt
new file mode 100644
index 00000000000..9465bfb8e0c
--- /dev/null
+++ b/build/pkgs/jupyter_jsmol/distros/conda.txt
@@ -0,0 +1 @@
+jupyter-jsmol
diff --git a/build/pkgs/jupyterlab_pygments/distros/conda.txt b/build/pkgs/jupyterlab_pygments/distros/conda.txt
new file mode 100644
index 00000000000..23254749a23
--- /dev/null
+++ b/build/pkgs/jupyterlab_pygments/distros/conda.txt
@@ -0,0 +1 @@
+jupyterlab_pygments
diff --git a/build/pkgs/mathics/distros/conda.txt b/build/pkgs/mathics/distros/conda.txt
new file mode 100644
index 00000000000..800ac5e8aa4
--- /dev/null
+++ b/build/pkgs/mathics/distros/conda.txt
@@ -0,0 +1 @@
+mathics3
diff --git a/build/pkgs/nbclient/distros/conda.txt b/build/pkgs/nbclient/distros/conda.txt
new file mode 100644
index 00000000000..66ffbb0ca10
--- /dev/null
+++ b/build/pkgs/nbclient/distros/conda.txt
@@ -0,0 +1 @@
+nbclient
diff --git a/build/pkgs/palettable/distros/conda.txt b/build/pkgs/palettable/distros/conda.txt
new file mode 100644
index 00000000000..646dd7426bb
--- /dev/null
+++ b/build/pkgs/palettable/distros/conda.txt
@@ -0,0 +1 @@
+palettable
diff --git a/build/pkgs/pathspec/distros/conda.txt b/build/pkgs/pathspec/distros/conda.txt
new file mode 100644
index 00000000000..6486958df08
--- /dev/null
+++ b/build/pkgs/pathspec/distros/conda.txt
@@ -0,0 +1 @@
+pathspec
diff --git a/build/pkgs/pint/distros/conda.txt b/build/pkgs/pint/distros/conda.txt
new file mode 100644
index 00000000000..45f523a5a6e
--- /dev/null
+++ b/build/pkgs/pint/distros/conda.txt
@@ -0,0 +1 @@
+pint
diff --git a/build/pkgs/platformdirs/distros/conda.txt b/build/pkgs/platformdirs/distros/conda.txt
new file mode 100644
index 00000000000..67fd014bbdd
--- /dev/null
+++ b/build/pkgs/platformdirs/distros/conda.txt
@@ -0,0 +1 @@
+platformdirs
diff --git a/build/pkgs/pluggy/distros/conda.txt b/build/pkgs/pluggy/distros/conda.txt
new file mode 100644
index 00000000000..11bdb5c1f5f
--- /dev/null
+++ b/build/pkgs/pluggy/distros/conda.txt
@@ -0,0 +1 @@
+pluggy
diff --git a/build/pkgs/poetry_core/distros/conda.txt b/build/pkgs/poetry_core/distros/conda.txt
new file mode 100644
index 00000000000..9b1f9e3fa7d
--- /dev/null
+++ b/build/pkgs/poetry_core/distros/conda.txt
@@ -0,0 +1 @@
+poetry-core
diff --git a/build/pkgs/pythran/distros/conda.txt b/build/pkgs/pythran/distros/conda.txt
new file mode 100644
index 00000000000..86d056b339f
--- /dev/null
+++ b/build/pkgs/pythran/distros/conda.txt
@@ -0,0 +1 @@
+pythran
diff --git a/build/pkgs/pytz_deprecation_shim/distros/conda.txt b/build/pkgs/pytz_deprecation_shim/distros/conda.txt
new file mode 100644
index 00000000000..2fd546ce62e
--- /dev/null
+++ b/build/pkgs/pytz_deprecation_shim/distros/conda.txt
@@ -0,0 +1 @@
+pytz-deprecation-shim
diff --git a/build/pkgs/setuptools_scm_git_archive/distros/conda.txt b/build/pkgs/setuptools_scm_git_archive/distros/conda.txt
new file mode 100644
index 00000000000..538474ff946
--- /dev/null
+++ b/build/pkgs/setuptools_scm_git_archive/distros/conda.txt
@@ -0,0 +1 @@
+setuptools-scm-git-archive
diff --git a/build/pkgs/texttable/distros/conda.txt b/build/pkgs/texttable/distros/conda.txt
new file mode 100644
index 00000000000..5d54c8a784d
--- /dev/null
+++ b/build/pkgs/texttable/distros/conda.txt
@@ -0,0 +1 @@
+texttable
diff --git a/build/pkgs/tinycss2/distros/conda.txt b/build/pkgs/tinycss2/distros/conda.txt
new file mode 100644
index 00000000000..29992f20d2c
--- /dev/null
+++ b/build/pkgs/tinycss2/distros/conda.txt
@@ -0,0 +1 @@
+tinycss2
diff --git a/build/pkgs/tomli/distros/conda.txt b/build/pkgs/tomli/distros/conda.txt
new file mode 100644
index 00000000000..aab392a3ac2
--- /dev/null
+++ b/build/pkgs/tomli/distros/conda.txt
@@ -0,0 +1 @@
+tomli
diff --git a/build/pkgs/tomlkit/distros/conda.txt b/build/pkgs/tomlkit/distros/conda.txt
new file mode 100644
index 00000000000..8141b831035
--- /dev/null
+++ b/build/pkgs/tomlkit/distros/conda.txt
@@ -0,0 +1 @@
+tomlkit
diff --git a/build/pkgs/typing_extensions/distros/conda.txt b/build/pkgs/typing_extensions/distros/conda.txt
new file mode 100644
index 00000000000..5fd4f05f341
--- /dev/null
+++ b/build/pkgs/typing_extensions/distros/conda.txt
@@ -0,0 +1 @@
+typing_extensions
diff --git a/build/pkgs/urllib3/distros/conda.txt b/build/pkgs/urllib3/distros/conda.txt
new file mode 100644
index 00000000000..a42590bebea
--- /dev/null
+++ b/build/pkgs/urllib3/distros/conda.txt
@@ -0,0 +1 @@
+urllib3
diff --git a/build/pkgs/virtualenv/distros/conda.txt b/build/pkgs/virtualenv/distros/conda.txt
new file mode 100644
index 00000000000..66072c76450
--- /dev/null
+++ b/build/pkgs/virtualenv/distros/conda.txt
@@ -0,0 +1 @@
+virtualenv

From 1c47261840fcee978b7471ff648a2b39eecde5fa Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 22:20:04 -0700
Subject: [PATCH 13/15] bootstrap-conda: Do not include pip lines for packages
 for which we have source directories

---
 bootstrap-conda | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bootstrap-conda b/bootstrap-conda
index cc9f02d0ec6..06c81e21521 100755
--- a/bootstrap-conda
+++ b/bootstrap-conda
@@ -97,7 +97,7 @@ DEVELOP_SYSTEM_PACKAGES="openssh pycodestyle pytest"
 (
     echo >&4 "  - pip:"
     echo >&5 "  - pip:"
-    for PKG_BASE in $(sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt) $(sage-package list :standard: :optional: --has-file install-requires.txt --no-file requirements.txt --no-file distros/conda.txt); do
+    for PKG_BASE in $((sage-package list :standard: :optional: --has-file requirements.txt --no-file distros/conda.txt --no-file src; sage-package list :standard: :optional: --has-file install-requires.txt --no-file requirements.txt --no-file distros/conda.txt --no-file src) | sort); do
         PKG_SCRIPTS=build/pkgs/$PKG_BASE
         SYSTEM_PACKAGES_FILE=$PKG_SCRIPTS/requirements.txt
         if [ ! -f $SYSTEM_PACKAGES_FILE ]; then

From 6d067200c54e48597c262695b866cc3c321ff766 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 5 Aug 2022 22:23:24 -0700
Subject: [PATCH 14/15] build/pkgs: Add even more distros/conda.txt files
 (fixup)

---
 build/pkgs/beniget/{ => distros}/conda.txt | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename build/pkgs/beniget/{ => distros}/conda.txt (100%)

diff --git a/build/pkgs/beniget/conda.txt b/build/pkgs/beniget/distros/conda.txt
similarity index 100%
rename from build/pkgs/beniget/conda.txt
rename to build/pkgs/beniget/distros/conda.txt

From d90b64c6b7957b6c2294a1f0efb0447fcce138fa Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Mon, 12 Sep 2022 11:27:17 -0700
Subject: [PATCH 15/15] Revert "build/pkgs/git_trac_command: New"

This reverts commit ac2c48db84c1a59e333552e5abfcdc3229fb9084.
---
 build/pkgs/git_trac_command/SPKG.rst         | 14 --------------
 build/pkgs/git_trac_command/requirements.txt |  1 -
 build/pkgs/git_trac_command/trees.txt        |  1 -
 build/pkgs/git_trac_command/type             |  1 -
 4 files changed, 17 deletions(-)
 delete mode 100644 build/pkgs/git_trac_command/SPKG.rst
 delete mode 100644 build/pkgs/git_trac_command/requirements.txt
 delete mode 100644 build/pkgs/git_trac_command/trees.txt
 delete mode 100644 build/pkgs/git_trac_command/type

diff --git a/build/pkgs/git_trac_command/SPKG.rst b/build/pkgs/git_trac_command/SPKG.rst
deleted file mode 100644
index d8da01bd818..00000000000
--- a/build/pkgs/git_trac_command/SPKG.rst
+++ /dev/null
@@ -1,14 +0,0 @@
-git_trac_command: Provides the subcommand "git trac"
-====================================================
-
-Description
------------
-
-This module implements a subcommand ``git trac``.
-See https://doc.sagemath.org/html/en/developer/git_trac.html
-
-
-Upstream Contact
-----------------
-
-https://github.com/sagemath/git-trac-command
diff --git a/build/pkgs/git_trac_command/requirements.txt b/build/pkgs/git_trac_command/requirements.txt
deleted file mode 100644
index 4f36b5eae53..00000000000
--- a/build/pkgs/git_trac_command/requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-git+https://github.com/sagemath/git-trac-command
diff --git a/build/pkgs/git_trac_command/trees.txt b/build/pkgs/git_trac_command/trees.txt
deleted file mode 100644
index b268580307d..00000000000
--- a/build/pkgs/git_trac_command/trees.txt
+++ /dev/null
@@ -1 +0,0 @@
-# Users should install this manually in their environment. It should not be installed in SAGE_VENV
diff --git a/build/pkgs/git_trac_command/type b/build/pkgs/git_trac_command/type
deleted file mode 100644
index 134d9bc32d5..00000000000
--- a/build/pkgs/git_trac_command/type
+++ /dev/null
@@ -1 +0,0 @@
-optional