debian/man: Mark other obsolescent commands as deprecated.

{eaddress,ecitmatch,econtact,edirect,edirutil,enotify,entrez-phrase-search,
eproxy,espell,ftp-cp,ftp-ls,protein-neighbors}.1: Mark as
deprecated (somewhat speculatively in the case of edirect), with
suggestions for alternatives in most cases.  All of these commands have
been around for a while, so they can remain in /usr/bin for bullseye.

13 files changed, 87 insertions, 25 deletions

diff --git a/debian/changelog b/debian/changelog
index bfa8ce0..e606705 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,8 +8,14 @@ ncbi-entrez-direct (14.6.20210224+dfsg-2) UNRELEASED; urgency=medium
     in having them appear in /usr/bin in bullseye only to disappear fully
     in the next stable Debian release.
   * debian/man: Drop corresponding man pages and references thereto.
-
- -- Aaron M. Ucko <ucko@debian.org>  Sun, 07 Mar 2021 15:03:01 -0500
+  * debian/man/{eaddress,ecitmatch,econtact,edirect,edirutil,enotify,
+    entrez-phrase-search,eproxy,espell,ftp-cp,ftp-ls,protein-neighbors}.1:
+    Mark as deprecated (somewhat speculatively in the case of edirect),
+    with suggestions for alternatives in most cases.  All of these
+    commands have been around for a while, so they can remain in /usr/bin
+    for bullseye.
+
+ -- Aaron M. Ucko <ucko@debian.org>  Sun, 07 Mar 2021 16:17:28 -0500
 
 ncbi-entrez-direct (14.6.20210224+dfsg-1) unstable; urgency=medium
 
diff --git a/debian/man/eaddress.1 b/debian/man/eaddress.1
index a68682a..8316f2f 100644
--- a/debian/man/eaddress.1
+++ b/debian/man/eaddress.1
@@ -1,11 +1,18 @@
-.TH EADDRESS 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.TH EADDRESS 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-eaddress \- check edirect's notion of your e\-mail address
+eaddress \- check edirect's notion of your e\-mail address (DEPRECATED)
 .SH SYNOPSIS
 .B eaddress
 
 .B edirect -address
 .SH DESCRIPTION
+\fBNote:\fP \fBeaddress\fP will not appear
+in future releases of NCBI Entrez Direct.
+However, several other commands, such as \fBeinfo\fP,
+take a \fB\-debug\fP flag
+that will reveal an \fBnquire\fP command line
+containing the email address they pass.
+
 \fBeaddress\fP prints (to standard output) the e\-mail address
 that other \fBedirect\fP(1) subcommands will send by default
 to have someone to notify in case
@@ -18,8 +25,10 @@ or reported by \fBwhoami\fP(1)
 with a hostname from \fB/etc/mailname\fP
 or \fBuname\fP(2),
 attempting to obtain a fully qualified form if necessary.
+
 .SH SEE ALSO
 .BR econtact (1),
 .BR edirect (1),
+.BR einfo (1),
 .BR whoami (1).
 
diff --git a/debian/man/ecitmatch.1 b/debian/man/ecitmatch.1
index 1b99aeb..7ba9ab1 100644
--- a/debian/man/ecitmatch.1
+++ b/debian/man/ecitmatch.1
@@ -1,6 +1,6 @@
-.TH ECITMATCH 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.TH ECITMATCH 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-ecitmatch \- look up a citation's PubMed ID
+ecitmatch \- look up a citation's PubMed ID (DEPRECATED)
 .SH SYNOPSIS
 \fBecitmatch\fP (\fBedirect\ \-citmatch\fP)
 [\|\fB\-help\fP\|]
@@ -10,6 +10,9 @@ ecitmatch \- look up a citation's PubMed ID
 [\|\fB\-page\fP\ \fIN\fP\|]
 [\|\fB\-author\fP\ \fIname\fP\|]
 .SH DESCRIPTION
+\fBNote:\fP \fBecitmatch\fP will not appear
+in future releases of NCBI Entrez Direct.
+
 \fBecitmatch\fP prints (to standard output)
 the numeric PubMed identifier for a specified article.
 If there were multiple matches, it substitutes
diff --git a/debian/man/econtact.1 b/debian/man/econtact.1
index 7ff4c29..4e41daa 100644
--- a/debian/man/econtact.1
+++ b/debian/man/econtact.1
@@ -1,12 +1,17 @@
-.TH ECONTACT 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.TH ECONTACT 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-econtact \- adjust contact information for an edirect pipeline
+econtact \- adjust contact information for an edirect pipeline (DEPRECATED)
 .SH SYNOPSIS
 \fBecontact\fP (\fBedirect\ \-contact\fP)
 [\|\fB\-help\fP\|]
 [\|\fB\-email\fP\ \fIaddress\fP\|]
 [\|\fB\-tool\fP\ \fIname\fP\|]
 .SH DESCRIPTION
+\fBNote:\fP \fBecontact\fP will not appear
+in future releases of NCBI Entrez Direct.
+Instead, please set the \fBEMAIL\fP environment variable appropriately,
+or supply explicit \fB\-email\fP settings to individual commands.
+
 \fBecontact\fP adjusts the e\-mail address and/or client name
 that subsequent \fBedirect\fP(1) pipeline stages will send
 to have someone to notify in case
diff --git a/debian/man/edirect.1 b/debian/man/edirect.1
index c229602..5a9db21 100644
--- a/debian/man/edirect.1
+++ b/debian/man/edirect.1
@@ -1,6 +1,6 @@
 .TH EDIRECT 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-edirect \- access NCBI Entrez from the command line
+edirect \- access NCBI Entrez from the command line (DEPRECATED)
 .SH SYNOPSIS
 .B edirect\ \-version
 
@@ -40,6 +40,12 @@ edirect \- access NCBI Entrez from the command line
 
 \fBedirect\ \-nquir\fP \fIoptions\fP
 .SH DESCRIPTION
+\fBNote:\fP \fBedirect\fP might not appear
+in future releases of NCBI Entrez Direct.
+However, several individual commands
+(\fBesearch\fP through \fBepost\fP)
+live on as \fBnquire\fP\-based shell scripts.
+
 \fBedirect\fP (Entrez Direct) is a command\-line utility
 for consulting NCBI's set of interconnected databases
 (publication, sequence, structure, gene, variation, expression, etc.)
diff --git a/debian/man/edirutil.1 b/debian/man/edirutil.1
index 9f78c78..942632e 100644
--- a/debian/man/edirutil.1
+++ b/debian/man/edirutil.1
@@ -1,6 +1,6 @@
-.TH EDIRUTIL 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.TH EDIRUTIL 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-edirutil \- synthesize NCBI ENTREZ_DIRECT XML (edirect pipeline state)
+edirutil \- synthesize NCBI ENTREZ_DIRECT XML (DEPRECATED)
 .SH SYNOPSIS
 .B edirutil
 [\|\fB\-db\fP\ \fIname\fP\|]
@@ -14,6 +14,10 @@ edirutil \- synthesize NCBI ENTREZ_DIRECT XML (edirect pipeline state)
 [\|\fB\-verbose\fP\|]
 [\|\fB\-debug\fP\|]
 .SH DESCRIPTION
+\fBNote:\fP \fBedirutil\fP will not appear
+in future releases of NCBI Entrez Direct.
+Instead, please supply explicit \fB\-web\fP settings to individual commands.
+
 \fBedirutil\fP synthesizes \fBENTREZ_DIRECT\fP XML records,
 which several \fBedirect\fP commands read, write, or both,
 to allow for server\-side transformation or filtering of results
diff --git a/debian/man/enotify.1 b/debian/man/enotify.1
index a19d189..fe9cf7c 100644
--- a/debian/man/enotify.1
+++ b/debian/man/enotify.1
@@ -1,12 +1,15 @@
-.TH ENOTIFY 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.TH ENOTIFY 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-enotify \- send e\-mail with NCBI Entrez search results
+enotify \- send e\-mail with NCBI Entrez search results (DEPRECATED)
 .SH SYNOPSIS
 \fBenotify\fP (\fBedirect\ \-notify\fP)
 [\|\fB\-help\fP\|]
 [\|\fB\-email\fP\ \fIaddress\fP\|]
 [\|\fB\-tool\fP\ \fIname\fP\|]
 .SH DESCRIPTION
+\fBNote:\fP \fBenotify\fP will not appear
+in future releases of NCBI Entrez Direct.
+
 \fBenotify\fP sends e\-mail with results
 of an \fBedirect\fP(1) search.
 .SH OPTIONS
diff --git a/debian/man/entrez-phrase-search.1 b/debian/man/entrez-phrase-search.1
index 7f975bb..c3efa10 100644
--- a/debian/man/entrez-phrase-search.1
+++ b/debian/man/entrez-phrase-search.1
@@ -1,6 +1,6 @@
-.TH ENTREZ-PHRASE-SEARCH 1 2019-02-06 NCBI "NCBI Entrez Direct User's Manual"
+.TH ENTREZ-PHRASE-SEARCH 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-entrez\-phrase\-search \- search NCBI Entrez for phrases
+entrez\-phrase\-search \- search NCBI Entrez for phrases (DEPRECATED)
 .SH SYNOPSIS
 \fBentrez\-phrase\-search\fP
 [\|\fB\-help\fP\|]
@@ -11,6 +11,12 @@ entrez\-phrase\-search \- search NCBI Entrez for phrases
 [\|\fB\-field\fP\ \fIname\fP\|]
 \fIquery\fP
 .SH DESCRIPTION
+\fBNote:\fP \fBentrez\-phrase\-search\fP will not appear
+in future releases of NCBI Entrez Direct.
+Instead, please either run \fBesearch\fP normally
+or establish a local archive via \fBarchive\-pubmed\fP
+and search it via \fBphrase\-search\fP.
+
 \fBentrez\-phrase\-search\fP
 is an \fBedirect\fP(1) \fBesearch\fP(1) wrapper script
 that searches an NCBI Entrez database for a phrase
diff --git a/debian/man/eproxy.1 b/debian/man/eproxy.1
index 204ca0f..470dcf0 100644
--- a/debian/man/eproxy.1
+++ b/debian/man/eproxy.1
@@ -1,12 +1,15 @@
-.TH EPROXY 1 2017-01-24 NCBI "NCBI Entrez Direct User's Manual"
+.TH EPROXY 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-eproxy \- load NCBI Entrez search aliases
+eproxy \- load NCBI Entrez search aliases (DEPRECATED)
 .SH SYNOPSIS
 \fBeproxy\fP (\fBedirect\ \-proxy\fP)
 [\|\fB\-help\fP\|]
 [\|\fB\-alias\fP\ \fIfilename\fP\|]
 [\|\fB\-pipe\fP\|]
 .SH DESCRIPTION
+\fBNote:\fP \fBeproxy\fP will not appear
+in future releases of NCBI Entrez Direct.
+
 \fBeproxy\fP loads named search term aliases
 for use in subsequent \fBedirect\fP pipeline stages,
 from a two\-column tab\-delimited text file.
diff --git a/debian/man/espell.1 b/debian/man/espell.1
index 6712d73..73931d8 100644
--- a/debian/man/espell.1
+++ b/debian/man/espell.1
@@ -1,12 +1,16 @@
-.TH ESPELL 1 2019-02-06 NCBI "NCBI Entrez Direct User's Manual"
+.TH ESPELL 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-espell \- spell\-correct an NCBI Entrez query
+espell \- spell\-correct an NCBI Entrez query (DEPRECATED)
 .SH SYNOPSIS
 \fBespell\fP (\fBedirect\ \-spell\fP)
 [\|\fB\-help\fP\|]
 \fB\-db\fP\ \fIname\fP
 \fB\-q\fP\|[\|\fBuery\fP\|]\fP\ \fIstr\fP
 .SH DESCRIPTION
+\fBNote:\fP \fBespell\fP will not appear
+in future releases of NCBI Entrez Direct.
+However, \fBesearch\fP continues to accept \fB\-spell\fP.
+
 \fBespell\fP produces an NCBI \fBeSpellResult\fP XML document
 indicating what changes, if any,
 \fBesearch \-spell\fP would make to the given query.
diff --git a/debian/man/ftp-cp.1 b/debian/man/ftp-cp.1
index c43c862..553412d 100644
--- a/debian/man/ftp-cp.1
+++ b/debian/man/ftp-cp.1
@@ -1,12 +1,16 @@
-.TH FTP-CP 1 2020-03-22 NCBI "NCBI Entrez Direct User's Manual"
+.TH FTP-CP 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-ftp\-cp \- download files from an FTP server
+ftp\-cp \- download files from an FTP server (DEPRECATED)
 .SH SYNOPSIS
 \fBftp\-cp\fP (\fBedirect\ \-ftpcp\fP)
 .I server
 .I dir
 [\|\fIfilename...\fP\|]
 .SH DESCRIPTION
+\fBNote:\fP \fBftp\-cp\fP will not appear
+in future releases of NCBI Entrez Direct.
+Instead, please use \fBnquire \-ftp\fP.
+
 \fBftp\-cp\fP downloads one or more files from a given directory
 on a specified file server.
 If no file names appear on the command line,
@@ -19,4 +23,5 @@ it will read the list of names to use from standard input.
 .BR edirect (1),
 .BR ftp\-ls (1),
 .BR index\-pubmed (1),
+.BR nquire (1),
 .BR rchive (1).
diff --git a/debian/man/ftp-ls.1 b/debian/man/ftp-ls.1
index 58a81ba..decf649 100644
--- a/debian/man/ftp-ls.1
+++ b/debian/man/ftp-ls.1
@@ -1,11 +1,15 @@
-.TH FTP-LS 1 2020-03-22 NCBI "NCBI Entrez Direct User's Manual"
+.TH FTP-LS 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-ftp\-ls \- list directory entries on an FTP server
+ftp\-ls \- list directory entries on an FTP server (DEPRECATED)
 .SH SYNOPSIS
 \fBftp\-ls\fP (\fBedirect\ \-ftpls\fP)
 .I server
 .I dir
 .SH DESCRIPTION
+\fBNote:\fP \fBftp\-ls\fP will not appear
+in future releases of NCBI Entrez Direct.
+Instead, please use \fBnquire \-lst\fP.
+
 \fBftp\-ls\fP lists the contents of a given directory
 on a specified file server.
 It prints one line per item,
diff --git a/debian/man/protein-neighbors.1 b/debian/man/protein-neighbors.1
index 482639b..670c289 100644
--- a/debian/man/protein-neighbors.1
+++ b/debian/man/protein-neighbors.1
@@ -1,9 +1,13 @@
-.TH PROTEIN-NEIGHBORS 1 2018-11-18 NCBI "NCBI Entrez Direct User's Manual"
+.TH PROTEIN-NEIGHBORS 1 2021-03-07 NCBI "NCBI Entrez Direct User's Manual"
 .SH NAME
-protein\-neighbors \- find similar protein accessions, via NCBI BLAST.
+protein\-neighbors \- find similar protein accessions, via BLAST (DEPRECATED)
 .SH SYNOPSIS
 \fBprotein\-neighbors\fP
 .SH DESCRIPTION
+\fBNote:\fP \fBprotein\-neighbors\fP will not appear
+in future releases of NCBI Entrez Direct.
+However, the key \fBeblast\fP script remains available for now.
+
 \fBprotein\-neighbors\fP reads one or more protein accessions
 from standard input
 and performs an online search for similar sequences